Starting phenix.real_space_refine on Sun Jul 5 21:56:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cwl_30482/07_2026/7cwl_30482.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19459 2.51 5 N 5120 2.21 5 O 5924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30638 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8358 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 1021} Chain breaks: 6 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8332 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 50, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8372 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1021} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.72, per 1000 atoms: 0.19 Number of scatterers: 30638 At special positions: 0 Unit cell: (171.6, 159.12, 212.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5924 8.00 N 5120 7.00 C 19459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.23 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.09 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7268 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 64 sheets defined 20.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.953A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.980A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.634A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.706A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.881A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.539A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.921A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.748A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.644A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 4.023A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.597A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.509A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.933A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.805A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.839A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.350A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.502A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.938A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.938A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.094A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.192A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.754A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.532A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.840A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.686A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.916A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.848A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.927A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR G 113 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.869A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN J 27 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS K 23 " --> pdb=" O THR K 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR K 74 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N ALA K 25 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR K 72 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN K 27 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP K 70 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 2742 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: 7.60 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7275 1.33 - 1.45: 7862 1.45 - 1.58: 16008 1.58 - 1.70: 1 1.70 - 1.83: 171 Bond restraints: 31317 Sorted by residual: bond pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 1.465 1.699 -0.234 1.10e-02 8.26e+03 4.52e+02 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.328 1.454 -0.126 1.26e-02 6.30e+03 9.96e+01 bond pdb=" CA SER A 60 " pdb=" CB SER A 60 " ideal model delta sigma weight residual 1.533 1.475 0.058 1.51e-02 4.39e+03 1.48e+01 bond pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.33e+01 bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 ... (remaining 31312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 42089 3.80 - 7.60: 474 7.60 - 11.40: 23 11.40 - 15.20: 0 15.20 - 19.00: 1 Bond angle restraints: 42587 Sorted by residual: angle pdb=" C THR A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 120.52 139.52 -19.00 9.90e-01 1.02e+00 3.68e+02 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 113.20 102.83 10.37 9.60e-01 1.09e+00 1.17e+02 angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS C 301 " pdb=" CA CYS C 301 " pdb=" C CYS C 301 " ideal model delta sigma weight residual 113.23 102.42 10.81 1.24e+00 6.50e-01 7.60e+01 angle pdb=" CA PRO A 589 " pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 112.00 100.80 11.20 1.40e+00 5.10e-01 6.40e+01 ... (remaining 42582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 17490 16.86 - 33.73: 718 33.73 - 50.59: 155 50.59 - 67.46: 42 67.46 - 84.32: 10 Dihedral angle restraints: 18415 sinusoidal: 7094 harmonic: 11321 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.02 73.02 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.90 72.90 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.34 72.34 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 18412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4317 0.097 - 0.194: 488 0.194 - 0.291: 73 0.291 - 0.388: 16 0.388 - 0.485: 4 Chirality restraints: 4898 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 4895 not shown) Planarity restraints: 5495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG C1301 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.315 2.00e-02 2.50e+03 2.68e-01 9.00e+02 pdb=" C7 NAG A1301 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " 0.309 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG A1303 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.032 2.00e-02 2.50e+03 ... (remaining 5492 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 28 2.15 - 2.84: 10324 2.84 - 3.52: 42688 3.52 - 4.21: 72136 4.21 - 4.90: 123118 Nonbonded interactions: 248294 Sorted by model distance: nonbonded pdb=" CD2 LEU B 48 " pdb=" CE2 PHE B 306 " model vdw 1.462 3.760 nonbonded pdb=" CE2 PHE A 329 " pdb=" SG CYS A 525 " model vdw 1.698 3.700 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 1.701 3.040 nonbonded pdb=" CD1 LEU C 48 " pdb=" O LYS C 304 " model vdw 1.804 3.460 nonbonded pdb=" OE2 GLU C 324 " pdb=" CG2 VAL C 534 " model vdw 1.848 3.460 ... (remaining 248289 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 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 38 or resid 44 through 407 or (res \ id 408 and (name N or name CA or name C or name O or name CB )) or resid 409 thr \ ough 1309)) selection = (chain 'B' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 527 or resid 530 t \ hrough 698 or (resid 699 and (name N or name CA or name C or name O or name CB ) \ ) or resid 700 through 1097 or (resid 1098 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1099 through 1309)) selection = (chain 'C' and (resid 14 through 38 or resid 44 through 331 or resid 335 through \ 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or r \ esid 358 through 407 or (resid 408 and (name N or name CA or name C or name O or \ name CB )) or resid 409 through 698 or (resid 699 and (name N or name CA or nam \ e C or name O or name CB )) or resid 700 through 1097 or (resid 1098 and (name N \ or name CA or name C or name O or name CB )) or resid 1099 through 1309)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = (chain 'L' and resid 1 through 107) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.000 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.730 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 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 : 0.009 0.234 31389 Z= 0.513 Angle : 1.097 19.004 42758 Z= 0.693 Chirality : 0.069 0.485 4898 Planarity : 0.011 0.300 5468 Dihedral : 10.201 84.319 11012 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.59 % Favored : 91.99 % Rotamer: Outliers : 1.07 % Allowed : 2.18 % Favored : 96.75 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.11), residues: 3846 helix: -3.14 (0.16), residues: 582 sheet: -2.18 (0.16), residues: 818 loop : -2.35 (0.10), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 61 TYR 0.030 0.003 TYR G 94 PHE 0.035 0.003 PHE C 392 TRP 0.025 0.003 TRP H 47 HIS 0.012 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.51 (31317) covalent geometry : angle 1.09252 / 0.69 (42587) SS BOND : bond 0.03265 / 1.40 ( 45) SS BOND : angle 2.19593 / 1.25 ( 90) hydrogen bonds : bond 0.25455 / 16.92 ( 1019) hydrogen bonds : angle 11.62462 / 8.07 ( 2742) link_NAG-ASN : bond 0.00197 / 0.13 ( 27) link_NAG-ASN : angle 1.47255 / 1.04 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 534 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.7788 (m-10) cc_final: 0.7531 (m-10) REVERT: A 592 PHE cc_start: 0.1984 (m-80) cc_final: 0.1744 (m-80) REVERT: A 900 MET cc_start: 0.6516 (mtp) cc_final: 0.6189 (ttm) REVERT: B 984 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5343 (mt) REVERT: B 1029 MET cc_start: 0.7133 (tpp) cc_final: 0.6901 (tpp) REVERT: C 54 LEU cc_start: 0.8988 (mt) cc_final: 0.8683 (mt) REVERT: C 1029 MET cc_start: 0.7625 (tpp) cc_final: 0.7186 (tpp) REVERT: G 72 ARG cc_start: 0.5347 (ptt90) cc_final: 0.5057 (mpt180) REVERT: L 22 THR cc_start: 0.8332 (m) cc_final: 0.7968 (p) REVERT: L 88 CYS cc_start: 0.0587 (p) cc_final: -0.0049 (p) outliers start: 36 outliers final: 11 residues processed: 564 average time/residue: 0.2017 time to fit residues: 179.4954 Evaluate side-chains 217 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 115 GLN A 146 HIS A 148 ASN A 282 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 121 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 784 GLN B 901 GLN B 913 GLN B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 122 ASN C 211 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN G 82 GLN G 84 ASN G 104 ASN H 13 GLN H 39 GLN H 84 ASN H 104 ASN I 84 ASN L 27 GLN L 55 GLN J 38 GLN K 38 GLN K 55 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.104944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.085487 restraints weight = 165579.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.083761 restraints weight = 170434.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.084082 restraints weight = 134356.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.084423 restraints weight = 105610.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.084516 restraints weight = 93286.208| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31389 Z= 0.181 Angle : 0.709 12.326 42758 Z= 0.368 Chirality : 0.047 0.350 4898 Planarity : 0.005 0.109 5468 Dihedral : 6.438 67.194 4209 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 2.30 % Allowed : 8.11 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.12), residues: 3846 helix: -0.48 (0.19), residues: 627 sheet: -1.39 (0.17), residues: 832 loop : -1.96 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 346 TYR 0.032 0.002 TYR G 53 PHE 0.029 0.002 PHE C 464 TRP 0.014 0.002 TRP C 886 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (31317) covalent geometry : angle 0.70192 / 0.37 (42587) SS BOND : bond 0.00453 / 0.28 ( 45) SS BOND : angle 1.65289 / 1.01 ( 90) hydrogen bonds : bond 0.04862 / 3.29 ( 1019) hydrogen bonds : angle 7.42729 / 5.13 ( 2742) link_NAG-ASN : bond 0.00430 / 0.29 ( 27) link_NAG-ASN : angle 1.72686 / 1.16 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 257 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 976 VAL cc_start: 0.7993 (t) cc_final: 0.7785 (t) REVERT: B 1029 MET cc_start: 0.7725 (tpp) cc_final: 0.7502 (ttm) REVERT: C 1029 MET cc_start: 0.8169 (tpp) cc_final: 0.7934 (tpp) REVERT: C 1089 PHE cc_start: 0.7797 (m-10) cc_final: 0.7481 (m-10) REVERT: G 72 ARG cc_start: 0.5169 (ptt90) cc_final: 0.4921 (mtt-85) REVERT: G 74 ASN cc_start: 0.4850 (p0) cc_final: 0.4519 (t0) REVERT: G 103 MET cc_start: 0.5203 (tpp) cc_final: 0.4566 (tpp) REVERT: H 28 THR cc_start: 0.6043 (p) cc_final: 0.5787 (t) REVERT: L 5 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7771 (p) REVERT: L 74 THR cc_start: 0.7641 (m) cc_final: 0.7170 (m) REVERT: L 89 GLN cc_start: 0.6780 (tt0) cc_final: 0.4957 (tt0) outliers start: 77 outliers final: 43 residues processed: 319 average time/residue: 0.1795 time to fit residues: 94.3804 Evaluate side-chains 219 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 124 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 359 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 238 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 148 ASN B 360 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 185 ASN C 211 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.100985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.081135 restraints weight = 163592.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.078797 restraints weight = 171118.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.079021 restraints weight = 160220.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.078953 restraints weight = 156939.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.079193 restraints weight = 121824.109| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 31389 Z= 0.218 Angle : 0.716 16.339 42758 Z= 0.362 Chirality : 0.048 0.481 4898 Planarity : 0.005 0.070 5468 Dihedral : 5.821 58.582 4201 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 2.68 % Allowed : 9.33 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 3846 helix: 0.31 (0.20), residues: 631 sheet: -1.30 (0.16), residues: 901 loop : -1.83 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.027 0.002 TYR G 53 PHE 0.024 0.002 PHE A 855 TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (31317) covalent geometry : angle 0.70165 / 0.36 (42587) SS BOND : bond 0.00313 / 0.21 ( 45) SS BOND : angle 1.28932 / 0.77 ( 90) hydrogen bonds : bond 0.04405 / 2.93 ( 1019) hydrogen bonds : angle 6.64743 / 4.58 ( 2742) link_NAG-ASN : bond 0.00931 / 0.72 ( 27) link_NAG-ASN : angle 3.14644 / 1.87 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 193 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 1029 MET cc_start: 0.8809 (tpp) cc_final: 0.8578 (tpp) REVERT: B 63 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 79 PHE cc_start: 0.5081 (t80) cc_final: 0.4877 (t80) REVERT: B 83 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6680 (t) REVERT: B 312 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 699 LEU cc_start: 0.7957 (mp) cc_final: 0.7533 (mt) REVERT: B 1041 ASP cc_start: 0.7297 (t0) cc_final: 0.7053 (t0) REVERT: C 153 MET cc_start: 0.5543 (ppp) cc_final: 0.4630 (tpt) REVERT: C 606 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7790 (t0) REVERT: C 1005 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7464 (tm-30) REVERT: G 72 ARG cc_start: 0.5479 (ptt90) cc_final: 0.5129 (mtt-85) REVERT: G 74 ASN cc_start: 0.5373 (p0) cc_final: 0.4875 (t0) REVERT: G 103 MET cc_start: 0.5878 (tpp) cc_final: 0.5465 (tpp) REVERT: H 103 MET cc_start: 0.8762 (mmm) cc_final: 0.8445 (mpp) outliers start: 90 outliers final: 48 residues processed: 267 average time/residue: 0.1731 time to fit residues: 77.8687 Evaluate side-chains 204 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain J residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 187 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 342 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 360 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.101212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.081092 restraints weight = 161148.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.078956 restraints weight = 173454.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.079237 restraints weight = 141282.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.079578 restraints weight = 110778.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.079661 restraints weight = 97117.361| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31389 Z= 0.143 Angle : 0.603 14.020 42758 Z= 0.304 Chirality : 0.044 0.313 4898 Planarity : 0.004 0.046 5468 Dihedral : 5.338 59.327 4199 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 2.18 % Allowed : 10.29 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3846 helix: 0.77 (0.21), residues: 632 sheet: -1.10 (0.17), residues: 881 loop : -1.68 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.019 0.001 TYR A 160 PHE 0.021 0.001 PHE C 464 TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (31317) covalent geometry : angle 0.58803 / 0.30 (42587) SS BOND : bond 0.00239 / 0.15 ( 45) SS BOND : angle 1.67197 / 0.92 ( 90) hydrogen bonds : bond 0.03727 / 2.51 ( 1019) hydrogen bonds : angle 6.07582 / 4.18 ( 2742) link_NAG-ASN : bond 0.00393 / 0.27 ( 27) link_NAG-ASN : angle 2.66721 / 1.74 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5790 (tpt) cc_final: 0.5552 (tpt) REVERT: A 191 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6228 (mp0) REVERT: A 731 MET cc_start: 0.8172 (ptm) cc_final: 0.7962 (ptp) REVERT: A 1029 MET cc_start: 0.8638 (tpp) cc_final: 0.8389 (tpp) REVERT: B 63 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 312 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 753 LEU cc_start: 0.8893 (tt) cc_final: 0.8683 (tt) REVERT: C 18 LEU cc_start: 0.0796 (OUTLIER) cc_final: 0.0371 (pp) REVERT: C 186 PHE cc_start: 0.8060 (m-80) cc_final: 0.7774 (m-80) REVERT: C 740 MET cc_start: 0.7494 (ppp) cc_final: 0.7219 (tmm) REVERT: G 103 MET cc_start: 0.5289 (tpp) cc_final: 0.4713 (tpp) REVERT: J 24 ARG cc_start: 0.6555 (tpp-160) cc_final: 0.6324 (tpp-160) outliers start: 73 outliers final: 42 residues processed: 247 average time/residue: 0.1837 time to fit residues: 76.6450 Evaluate side-chains 199 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 213 optimal weight: 0.0020 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 251 optimal weight: 0.0370 chunk 310 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 overall best weight: 2.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN A 969 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.099026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.079076 restraints weight = 160917.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077062 restraints weight = 151253.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077383 restraints weight = 148770.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077400 restraints weight = 119616.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077568 restraints weight = 104804.585| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31389 Z= 0.210 Angle : 0.639 11.698 42758 Z= 0.326 Chirality : 0.045 0.274 4898 Planarity : 0.004 0.046 5468 Dihedral : 5.395 59.670 4199 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 2.83 % Allowed : 10.95 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3846 helix: 0.62 (0.20), residues: 648 sheet: -1.23 (0.16), residues: 922 loop : -1.62 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.022 0.002 TYR C 313 PHE 0.022 0.002 PHE B 157 TRP 0.020 0.002 TRP C 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (31317) covalent geometry : angle 0.63023 / 0.32 (42587) SS BOND : bond 0.00321 / 0.22 ( 45) SS BOND : angle 1.46043 / 0.79 ( 90) hydrogen bonds : bond 0.03944 / 2.62 ( 1019) hydrogen bonds : angle 6.08049 / 4.17 ( 2742) link_NAG-ASN : bond 0.00408 / 0.28 ( 27) link_NAG-ASN : angle 2.06478 / 1.41 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 157 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6016 (tpt) cc_final: 0.5788 (tpt) REVERT: A 191 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6732 (mt-10) REVERT: A 731 MET cc_start: 0.8428 (ptm) cc_final: 0.8163 (ptp) REVERT: B 63 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8729 (p) REVERT: B 157 PHE cc_start: 0.6997 (p90) cc_final: 0.6409 (p90) REVERT: B 312 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 364 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7472 (t0) REVERT: B 1041 ASP cc_start: 0.7072 (t0) cc_final: 0.6750 (t0) REVERT: C 18 LEU cc_start: 0.0871 (OUTLIER) cc_final: 0.0577 (pp) REVERT: C 1005 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7450 (tm-30) REVERT: G 74 ASN cc_start: 0.4999 (p0) cc_final: 0.4775 (m-40) REVERT: H 103 MET cc_start: 0.8788 (mmm) cc_final: 0.8402 (mpp) outliers start: 95 outliers final: 55 residues processed: 237 average time/residue: 0.1754 time to fit residues: 71.6578 Evaluate side-chains 196 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 104 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 301 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.097396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.077698 restraints weight = 160440.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075178 restraints weight = 155196.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.075666 restraints weight = 130803.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.075708 restraints weight = 104693.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.075751 restraints weight = 98991.708| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 31389 Z= 0.226 Angle : 0.652 12.121 42758 Z= 0.331 Chirality : 0.045 0.372 4898 Planarity : 0.004 0.048 5468 Dihedral : 5.452 59.632 4199 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 2.95 % Allowed : 11.30 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3846 helix: 0.52 (0.20), residues: 660 sheet: -1.26 (0.16), residues: 903 loop : -1.64 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.024 0.002 TYR G 94 PHE 0.019 0.002 PHE B 392 TRP 0.019 0.002 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (31317) covalent geometry : angle 0.63941 / 0.33 (42587) SS BOND : bond 0.00293 / 0.20 ( 45) SS BOND : angle 1.74523 / 0.97 ( 90) hydrogen bonds : bond 0.03933 / 2.64 ( 1019) hydrogen bonds : angle 6.08009 / 4.17 ( 2742) link_NAG-ASN : bond 0.00360 / 0.24 ( 27) link_NAG-ASN : angle 2.39672 / 1.50 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 149 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6547 (tpt) cc_final: 0.6240 (tpt) REVERT: A 191 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 224 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8250 (pp20) REVERT: A 275 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: A 731 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8278 (ptp) REVERT: B 63 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 157 PHE cc_start: 0.6852 (p90) cc_final: 0.6299 (p90) REVERT: B 364 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7787 (t0) REVERT: B 740 MET cc_start: 0.7001 (tpt) cc_final: 0.6719 (tpp) REVERT: B 1041 ASP cc_start: 0.7106 (t0) cc_final: 0.6800 (t0) REVERT: C 18 LEU cc_start: 0.0819 (OUTLIER) cc_final: 0.0524 (pp) REVERT: C 1005 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7531 (tm-30) REVERT: G 74 ASN cc_start: 0.5285 (p0) cc_final: 0.4944 (m-40) REVERT: G 94 TYR cc_start: 0.2033 (OUTLIER) cc_final: 0.1570 (t80) outliers start: 99 outliers final: 66 residues processed: 233 average time/residue: 0.1709 time to fit residues: 68.1296 Evaluate side-chains 211 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 285 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 327 optimal weight: 20.0000 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 307 optimal weight: 0.7980 chunk 311 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN G 39 GLN ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.098468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.078888 restraints weight = 160920.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076586 restraints weight = 166109.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077046 restraints weight = 138333.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077213 restraints weight = 102993.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077372 restraints weight = 93668.531| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31389 Z= 0.131 Angle : 0.584 12.655 42758 Z= 0.295 Chirality : 0.043 0.258 4898 Planarity : 0.004 0.046 5468 Dihedral : 5.085 59.120 4199 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 1.88 % Allowed : 12.82 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3846 helix: 0.89 (0.20), residues: 656 sheet: -1.09 (0.16), residues: 893 loop : -1.52 (0.12), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.021 0.001 TYR A 170 PHE 0.019 0.001 PHE B 392 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (31317) covalent geometry : angle 0.57238 / 0.29 (42587) SS BOND : bond 0.00228 / 0.16 ( 45) SS BOND : angle 2.04141 / 0.96 ( 90) hydrogen bonds : bond 0.03539 / 2.38 ( 1019) hydrogen bonds : angle 5.75304 / 3.94 ( 2742) link_NAG-ASN : bond 0.00305 / 0.21 ( 27) link_NAG-ASN : angle 1.80939 / 1.18 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6344 (tpt) cc_final: 0.6048 (tpt) REVERT: A 191 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 731 MET cc_start: 0.8466 (ptm) cc_final: 0.8246 (ptp) REVERT: B 63 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 157 PHE cc_start: 0.6998 (p90) cc_final: 0.6351 (p90) REVERT: B 364 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7639 (t0) REVERT: B 740 MET cc_start: 0.6699 (tpt) cc_final: 0.6448 (tpp) REVERT: B 1041 ASP cc_start: 0.6855 (t0) cc_final: 0.6580 (t0) REVERT: C 18 LEU cc_start: 0.1068 (OUTLIER) cc_final: 0.0728 (pp) REVERT: C 954 GLN cc_start: 0.7763 (mt0) cc_final: 0.7524 (mt0) REVERT: C 1005 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7386 (tm-30) REVERT: G 94 TYR cc_start: 0.2251 (OUTLIER) cc_final: 0.1695 (t80) REVERT: H 103 MET cc_start: 0.8732 (mmm) cc_final: 0.8440 (mpp) outliers start: 63 outliers final: 46 residues processed: 215 average time/residue: 0.1647 time to fit residues: 61.3024 Evaluate side-chains 195 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 40 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 99 optimal weight: 0.0570 chunk 168 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 212 optimal weight: 0.0470 chunk 193 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.097788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.078319 restraints weight = 160508.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.076343 restraints weight = 156783.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.076715 restraints weight = 147832.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.076662 restraints weight = 129499.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077047 restraints weight = 101618.669| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31389 Z= 0.158 Angle : 0.596 12.445 42758 Z= 0.302 Chirality : 0.043 0.239 4898 Planarity : 0.004 0.046 5468 Dihedral : 5.048 58.096 4198 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 2.00 % Allowed : 13.21 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 3846 helix: 0.91 (0.20), residues: 656 sheet: -1.07 (0.16), residues: 909 loop : -1.48 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 24 TYR 0.020 0.001 TYR A 170 PHE 0.020 0.001 PHE A 275 TRP 0.016 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (31317) covalent geometry : angle 0.58531 / 0.30 (42587) SS BOND : bond 0.00214 / 0.15 ( 45) SS BOND : angle 1.94326 / 0.90 ( 90) hydrogen bonds : bond 0.03596 / 2.40 ( 1019) hydrogen bonds : angle 5.72191 / 3.92 ( 2742) link_NAG-ASN : bond 0.00280 / 0.18 ( 27) link_NAG-ASN : angle 1.74961 / 1.17 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 156 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6292 (tpt) cc_final: 0.5929 (tpt) REVERT: A 731 MET cc_start: 0.8534 (ptm) cc_final: 0.8247 (ptp) REVERT: B 79 PHE cc_start: 0.5331 (t80) cc_final: 0.5128 (t80) REVERT: B 157 PHE cc_start: 0.7023 (p90) cc_final: 0.6261 (p90) REVERT: B 210 ILE cc_start: 0.5588 (OUTLIER) cc_final: 0.5385 (pt) REVERT: B 364 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7640 (t0) REVERT: B 740 MET cc_start: 0.6481 (tpt) cc_final: 0.6132 (tpp) REVERT: B 1041 ASP cc_start: 0.6882 (t0) cc_final: 0.6607 (t0) REVERT: C 18 LEU cc_start: 0.1288 (OUTLIER) cc_final: 0.0918 (pp) REVERT: C 1005 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7381 (tm-30) REVERT: G 94 TYR cc_start: 0.2344 (OUTLIER) cc_final: 0.1716 (t80) outliers start: 67 outliers final: 52 residues processed: 210 average time/residue: 0.1745 time to fit residues: 63.1621 Evaluate side-chains 199 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 140 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 354 optimal weight: 10.0000 chunk 374 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN J 38 GLN J 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.095541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.075649 restraints weight = 160348.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.073081 restraints weight = 154734.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073768 restraints weight = 129201.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073685 restraints weight = 106202.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073812 restraints weight = 97872.661| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 31389 Z= 0.265 Angle : 0.712 15.079 42758 Z= 0.361 Chirality : 0.046 0.477 4898 Planarity : 0.004 0.050 5468 Dihedral : 5.515 57.519 4197 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 2.21 % Allowed : 13.42 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3846 helix: 0.40 (0.20), residues: 659 sheet: -1.22 (0.16), residues: 923 loop : -1.63 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 72 TYR 0.023 0.002 TYR A 170 PHE 0.025 0.002 PHE B 497 TRP 0.018 0.002 TRP C 886 HIS 0.006 0.002 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.27 (31317) covalent geometry : angle 0.69677 / 0.36 (42587) SS BOND : bond 0.00352 / 0.23 ( 45) SS BOND : angle 2.08661 / 1.02 ( 90) hydrogen bonds : bond 0.04151 / 2.77 ( 1019) hydrogen bonds : angle 6.17886 / 4.25 ( 2742) link_NAG-ASN : bond 0.00408 / 0.26 ( 27) link_NAG-ASN : angle 2.69997 / 1.62 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 143 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6812 (tpt) cc_final: 0.6537 (tpt) REVERT: A 592 PHE cc_start: 0.5690 (m-10) cc_final: 0.4580 (m-10) REVERT: B 79 PHE cc_start: 0.5598 (t80) cc_final: 0.5338 (t80) REVERT: B 157 PHE cc_start: 0.7042 (p90) cc_final: 0.6203 (p90) REVERT: B 364 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7754 (t0) REVERT: B 731 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7750 (ptp) REVERT: B 1041 ASP cc_start: 0.7032 (t0) cc_final: 0.6813 (t0) REVERT: B 1101 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5060 (m90) REVERT: C 18 LEU cc_start: 0.1389 (OUTLIER) cc_final: 0.1091 (pp) REVERT: C 740 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7346 (tmm) REVERT: C 1005 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7598 (tm-30) REVERT: G 94 TYR cc_start: 0.2174 (OUTLIER) cc_final: 0.1701 (t80) outliers start: 74 outliers final: 56 residues processed: 198 average time/residue: 0.1721 time to fit residues: 59.2089 Evaluate side-chains 188 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 126 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 280 optimal weight: 0.9990 chunk 290 optimal weight: 0.6980 chunk 375 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN G 104 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.097660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.078367 restraints weight = 158941.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.076561 restraints weight = 159657.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077043 restraints weight = 132162.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077262 restraints weight = 96380.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077333 restraints weight = 89237.152| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31389 Z= 0.116 Angle : 0.598 13.132 42758 Z= 0.301 Chirality : 0.043 0.364 4898 Planarity : 0.004 0.048 5468 Dihedral : 5.057 58.496 4197 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 1.46 % Allowed : 14.14 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3846 helix: 0.82 (0.20), residues: 662 sheet: -1.07 (0.16), residues: 928 loop : -1.49 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 72 TYR 0.022 0.001 TYR A 396 PHE 0.028 0.001 PHE H 27 TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (31317) covalent geometry : angle 0.58728 / 0.30 (42587) SS BOND : bond 0.00228 / 0.15 ( 45) SS BOND : angle 1.61792 / 0.78 ( 90) hydrogen bonds : bond 0.03510 / 2.34 ( 1019) hydrogen bonds : angle 5.64705 / 3.88 ( 2742) link_NAG-ASN : bond 0.00308 / 0.22 ( 27) link_NAG-ASN : angle 2.07611 / 1.28 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6069 (tpt) cc_final: 0.5786 (tpt) REVERT: A 773 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 157 PHE cc_start: 0.6780 (p90) cc_final: 0.5960 (p90) REVERT: B 364 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7676 (t0) REVERT: B 753 LEU cc_start: 0.9014 (tt) cc_final: 0.8752 (tt) REVERT: B 950 ASP cc_start: 0.7137 (t70) cc_final: 0.6830 (t0) REVERT: C 18 LEU cc_start: 0.2221 (OUTLIER) cc_final: 0.1829 (pp) REVERT: C 740 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7012 (tmm) REVERT: C 1005 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7313 (tm-30) REVERT: G 94 TYR cc_start: 0.2470 (OUTLIER) cc_final: 0.1747 (t80) outliers start: 49 outliers final: 39 residues processed: 201 average time/residue: 0.1754 time to fit residues: 60.9277 Evaluate side-chains 184 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 158 optimal weight: 8.9990 chunk 363 optimal weight: 30.0000 chunk 257 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 147 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 356 optimal weight: 40.0000 chunk 216 optimal weight: 0.0370 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN G 57 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.097394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.077997 restraints weight = 160543.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.075912 restraints weight = 157667.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.076302 restraints weight = 136721.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076557 restraints weight = 100722.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.076669 restraints weight = 93236.086| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31389 Z= 0.128 Angle : 0.603 13.363 42758 Z= 0.302 Chirality : 0.043 0.343 4898 Planarity : 0.004 0.048 5468 Dihedral : 4.939 57.497 4197 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 1.64 % Allowed : 14.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3846 helix: 0.94 (0.21), residues: 657 sheet: -0.91 (0.16), residues: 907 loop : -1.46 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.022 0.001 TYR H 59 PHE 0.028 0.001 PHE H 27 TRP 0.013 0.001 TRP C 886 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (31317) covalent geometry : angle 0.59319 / 0.30 (42587) SS BOND : bond 0.00221 / 0.15 ( 45) SS BOND : angle 1.61954 / 0.78 ( 90) hydrogen bonds : bond 0.03497 / 2.31 ( 1019) hydrogen bonds : angle 5.57288 / 3.84 ( 2742) link_NAG-ASN : bond 0.00261 / 0.18 ( 27) link_NAG-ASN : angle 1.92846 / 1.21 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5074.65 seconds wall clock time: 88 minutes 58.55 seconds (5338.55 seconds total)