Starting phenix.real_space_refine on Fri Mar 6 11:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cwl_30482/03_2026/7cwl_30482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwl_30482/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cwl_30482/03_2026/7cwl_30482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwl_30482/03_2026/7cwl_30482.map" model { file = "/net/cci-nas-00/data/ceres_data/7cwl_30482/03_2026/7cwl_30482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwl_30482/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 27 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 dihedrals: 27 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.38, per 1000 atoms: 0.24 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: 2.59 Conformation dependent library (CDL) restraints added in 1.4 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: 1.72 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: 9.70 Time building geometry restraints manager: 3.45 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: 18033 16.86 - 33.73: 730 33.73 - 50.59: 165 50.59 - 67.46: 44 67.46 - 84.32: 10 Dihedral angle restraints: 18982 sinusoidal: 7661 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 18979 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.020 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 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 : 10.152 84.319 11579 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 covalent geometry : bond 0.00873 (31317) covalent geometry : angle 1.09252 (42587) SS BOND : bond 0.03265 ( 45) SS BOND : angle 2.19593 ( 90) hydrogen bonds : bond 0.25455 ( 1019) hydrogen bonds : angle 11.62462 ( 2742) link_NAG-ASN : bond 0.00197 ( 27) link_NAG-ASN : angle 1.47255 ( 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 : 0.752 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: 0.2011 time to fit residues: 178.2965 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 : 1.099 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 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 = 0.4281 r_free = 0.4281 target = 0.105043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.085849 restraints weight = 165697.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.084356 restraints weight = 168807.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.084818 restraints weight = 126622.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.085006 restraints weight = 100458.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.085069 restraints weight = 90399.388| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31389 Z= 0.166 Angle : 0.709 12.011 42758 Z= 0.367 Chirality : 0.047 0.236 4898 Planarity : 0.005 0.107 5468 Dihedral : 6.803 66.826 4776 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 2.27 % Allowed : 8.02 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.34 (0.12), residues: 3846 helix: -0.51 (0.19), residues: 626 sheet: -1.42 (0.17), residues: 835 loop : -1.97 (0.11), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.031 0.002 TYR G 53 PHE 0.029 0.002 PHE C 464 TRP 0.015 0.002 TRP C 64 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00364 (31317) covalent geometry : angle 0.70207 (42587) SS BOND : bond 0.00392 ( 45) SS BOND : angle 1.72754 ( 90) hydrogen bonds : bond 0.04862 ( 1019) hydrogen bonds : angle 7.47090 ( 2742) link_NAG-ASN : bond 0.00411 ( 27) link_NAG-ASN : angle 1.80389 ( 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 325 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 1.018 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: B 902 MET cc_start: 0.8465 (tpp) cc_final: 0.8206 (mmt) REVERT: B 976 VAL cc_start: 0.7996 (t) cc_final: 0.7787 (t) REVERT: B 1050 MET cc_start: 0.7446 (ptp) cc_final: 0.7241 (ptp) REVERT: C 1029 MET cc_start: 0.8258 (tpp) cc_final: 0.7993 (tpp) REVERT: C 1089 PHE cc_start: 0.7795 (m-10) cc_final: 0.7496 (m-10) REVERT: G 72 ARG cc_start: 0.5086 (ptt90) cc_final: 0.4876 (mtt90) REVERT: G 103 MET cc_start: 0.4859 (tpp) cc_final: 0.4230 (tpp) REVERT: H 28 THR cc_start: 0.5928 (p) cc_final: 0.5682 (t) outliers start: 76 outliers final: 44 residues processed: 310 average time/residue: 0.1843 time to fit residues: 94.4040 Evaluate side-chains 221 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 70 VAL 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 597 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL 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 1141 LEU Chi-restraints excluded: chain C residue 70 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 539 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 716 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 L residue 27 GLN Chi-restraints excluded: chain L residue 73 LEU 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: 9.9990 chunk 43 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 366 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 359 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 314 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN H 35 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.102368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.082551 restraints weight = 164114.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080575 restraints weight = 163810.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.080703 restraints weight = 152942.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080672 restraints weight = 152854.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080910 restraints weight = 114868.493| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31389 Z= 0.186 Angle : 0.678 19.410 42758 Z= 0.342 Chirality : 0.046 0.362 4898 Planarity : 0.004 0.057 5468 Dihedral : 6.290 59.958 4768 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.57 % Rotamer: Outliers : 2.39 % Allowed : 9.13 % Favored : 88.49 % 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: -1.88 (0.13), residues: 3846 helix: 0.47 (0.20), residues: 628 sheet: -1.32 (0.16), residues: 898 loop : -1.76 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.022 0.002 TYR G 53 PHE 0.024 0.002 PHE C 464 TRP 0.015 0.002 TRP B 886 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00401 (31317) covalent geometry : angle 0.66005 (42587) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.16311 ( 90) hydrogen bonds : bond 0.04218 ( 1019) hydrogen bonds : angle 6.52169 ( 2742) link_NAG-ASN : bond 0.01196 ( 27) link_NAG-ASN : angle 3.48919 ( 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 278 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 198 time to evaluate : 1.055 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 177 MET cc_start: 0.6048 (ptm) cc_final: 0.5254 (mmm) REVERT: A 731 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8136 (ptp) REVERT: A 1029 MET cc_start: 0.8741 (tpp) cc_final: 0.8444 (tpp) REVERT: B 53 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: B 63 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 312 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8130 (tt) REVERT: C 153 MET cc_start: 0.5446 (ppp) cc_final: 0.5122 (tmm) REVERT: C 258 TRP cc_start: 0.4696 (OUTLIER) cc_final: 0.4421 (p90) REVERT: C 298 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: C 606 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7836 (t0) REVERT: C 1005 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7402 (tm-30) REVERT: G 103 MET cc_start: 0.5884 (tpp) cc_final: 0.5075 (tpp) outliers start: 80 outliers final: 38 residues processed: 261 average time/residue: 0.1704 time to fit residues: 75.0752 Evaluate side-chains 200 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 731 MET 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 1115 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP 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 233 ILE Chi-restraints excluded: chain C residue 258 TRP 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 708 SER Chi-restraints excluded: chain C residue 724 THR 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 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: 0.8980 chunk 342 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 226 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 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** C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN G 57 ASN ** I 99 HIS ** 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 = 0.4241 r_free = 0.4241 target = 0.102913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.084170 restraints weight = 161964.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.082801 restraints weight = 174647.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.083155 restraints weight = 139376.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083398 restraints weight = 105492.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.083579 restraints weight = 94659.610| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31389 Z= 0.114 Angle : 0.584 14.585 42758 Z= 0.294 Chirality : 0.043 0.321 4898 Planarity : 0.004 0.042 5468 Dihedral : 5.812 59.871 4766 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 2.21 % Allowed : 10.23 % Favored : 87.56 % 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: -1.58 (0.13), residues: 3846 helix: 0.91 (0.21), residues: 635 sheet: -1.17 (0.16), residues: 941 loop : -1.60 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.017 0.001 TYR C 170 PHE 0.023 0.001 PHE C 464 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (31317) covalent geometry : angle 0.57205 (42587) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.44617 ( 90) hydrogen bonds : bond 0.03628 ( 1019) hydrogen bonds : angle 5.99427 ( 2742) link_NAG-ASN : bond 0.00392 ( 27) link_NAG-ASN : angle 2.34121 ( 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 264 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 1.001 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 191 GLU cc_start: 0.6533 (mt-10) cc_final: 0.6161 (mp0) REVERT: A 731 MET cc_start: 0.8147 (ptm) cc_final: 0.7930 (ptp) REVERT: A 1029 MET cc_start: 0.8500 (tpp) cc_final: 0.8220 (tpp) REVERT: B 53 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: B 63 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 312 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 753 LEU cc_start: 0.8864 (tt) cc_final: 0.8610 (tt) REVERT: B 1041 ASP cc_start: 0.6846 (t0) cc_final: 0.6401 (t0) REVERT: C 18 LEU cc_start: 0.1055 (OUTLIER) cc_final: 0.0724 (pp) REVERT: C 70 VAL cc_start: 0.3664 (OUTLIER) cc_final: 0.3239 (p) REVERT: C 258 TRP cc_start: 0.4748 (OUTLIER) cc_final: 0.4473 (p90) REVERT: C 740 MET cc_start: 0.7384 (ppp) cc_final: 0.7098 (tmm) REVERT: J 24 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.6080 (tpp-160) outliers start: 74 outliers final: 41 residues processed: 251 average time/residue: 0.1717 time to fit residues: 72.5597 Evaluate side-chains 201 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 ILE 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 759 PHE 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 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR 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 699 LEU 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 70 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 616 ASN 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 788 ILE 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 29 ILE Chi-restraints excluded: chain J residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 251 optimal weight: 0.2980 chunk 310 optimal weight: 0.0770 chunk 370 optimal weight: 20.0000 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 211 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.100173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.080002 restraints weight = 161623.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.078126 restraints weight = 157873.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.078538 restraints weight = 135755.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078693 restraints weight = 102563.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.078788 restraints weight = 95151.721| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31389 Z= 0.191 Angle : 0.630 11.653 42758 Z= 0.320 Chirality : 0.044 0.306 4898 Planarity : 0.004 0.037 5468 Dihedral : 5.959 59.312 4766 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 2.74 % Allowed : 10.77 % Favored : 86.49 % 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: -1.57 (0.13), residues: 3846 helix: 0.87 (0.21), residues: 632 sheet: -1.19 (0.16), residues: 956 loop : -1.57 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.020 0.002 TYR C 313 PHE 0.020 0.002 PHE C 464 TRP 0.013 0.001 TRP C 886 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00418 (31317) covalent geometry : angle 0.61803 (42587) SS BOND : bond 0.00261 ( 45) SS BOND : angle 1.68555 ( 90) hydrogen bonds : bond 0.03821 ( 1019) hydrogen bonds : angle 5.98020 ( 2742) link_NAG-ASN : bond 0.00362 ( 27) link_NAG-ASN : angle 2.38713 ( 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 260 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 168 time to evaluate : 1.191 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 731 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8039 (ptp) REVERT: B 53 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: B 63 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 364 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7020 (t0) REVERT: C 18 LEU cc_start: 0.0960 (OUTLIER) cc_final: 0.0658 (pp) REVERT: C 740 MET cc_start: 0.7656 (ppp) cc_final: 0.7448 (tmm) REVERT: G 94 TYR cc_start: 0.2309 (OUTLIER) cc_final: 0.2063 (t80) outliers start: 92 outliers final: 51 residues processed: 244 average time/residue: 0.1755 time to fit residues: 73.4013 Evaluate side-chains 201 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 178 ASP 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 731 MET 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 969 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 SER 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 708 SER Chi-restraints excluded: chain B residue 747 THR 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 1141 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 213 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 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 G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR 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: 4.9990 chunk 322 optimal weight: 30.0000 chunk 190 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 335 optimal weight: 0.1980 chunk 301 optimal weight: 0.9980 chunk 327 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 273 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN A 969 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.101742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081575 restraints weight = 160657.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.079556 restraints weight = 173310.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079960 restraints weight = 129426.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080241 restraints weight = 100648.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080361 restraints weight = 91832.520| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31389 Z= 0.101 Angle : 0.556 10.452 42758 Z= 0.281 Chirality : 0.043 0.243 4898 Planarity : 0.003 0.041 5468 Dihedral : 5.562 59.980 4766 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 1.79 % Allowed : 11.66 % Favored : 86.55 % 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: -1.34 (0.13), residues: 3846 helix: 1.19 (0.21), residues: 631 sheet: -1.07 (0.16), residues: 965 loop : -1.44 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.018 0.001 TYR A 170 PHE 0.022 0.001 PHE C 464 TRP 0.012 0.001 TRP C 258 HIS 0.020 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00218 (31317) covalent geometry : angle 0.54978 (42587) SS BOND : bond 0.00214 ( 45) SS BOND : angle 1.07259 ( 90) hydrogen bonds : bond 0.03420 ( 1019) hydrogen bonds : angle 5.58590 ( 2742) link_NAG-ASN : bond 0.00325 ( 27) link_NAG-ASN : angle 1.79625 ( 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 238 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 1.184 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 191 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6151 (mt-10) REVERT: B 53 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: B 63 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 1041 ASP cc_start: 0.7134 (t0) cc_final: 0.6862 (t0) REVERT: C 18 LEU cc_start: 0.1009 (OUTLIER) cc_final: 0.0663 (pp) REVERT: C 712 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8104 (tt) REVERT: C 1005 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7299 (tm-30) REVERT: G 94 TYR cc_start: 0.2283 (OUTLIER) cc_final: 0.1752 (t80) REVERT: G 103 MET cc_start: 0.4809 (tpp) cc_final: 0.4245 (tpp) REVERT: H 103 MET cc_start: 0.8753 (mmm) cc_final: 0.8157 (mpp) REVERT: J 24 ARG cc_start: 0.7149 (tpp-160) cc_final: 0.6850 (tpp-160) outliers start: 60 outliers final: 31 residues processed: 227 average time/residue: 0.1765 time to fit residues: 68.0911 Evaluate side-chains 183 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 307 THR 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 896 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 130 VAL 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 1001 LEU Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU 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 712 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 285 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 150 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 311 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 317 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS ** J 90 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.099886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.079964 restraints weight = 161019.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.077665 restraints weight = 169036.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078116 restraints weight = 138612.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.078263 restraints weight = 106005.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.078403 restraints weight = 97598.969| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31389 Z= 0.164 Angle : 0.605 12.553 42758 Z= 0.305 Chirality : 0.044 0.358 4898 Planarity : 0.004 0.040 5468 Dihedral : 5.664 59.770 4765 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 1.97 % Allowed : 11.81 % 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: -1.28 (0.13), residues: 3846 helix: 1.09 (0.21), residues: 641 sheet: -0.97 (0.16), residues: 909 loop : -1.40 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.020 0.001 TYR A 170 PHE 0.019 0.001 PHE C 464 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00364 (31317) covalent geometry : angle 0.59273 (42587) SS BOND : bond 0.00234 ( 45) SS BOND : angle 1.71939 ( 90) hydrogen bonds : bond 0.03643 ( 1019) hydrogen bonds : angle 5.71642 ( 2742) link_NAG-ASN : bond 0.00324 ( 27) link_NAG-ASN : angle 2.30372 ( 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 227 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 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: 0.6053 (tpt) cc_final: 0.5803 (tpt) REVERT: A 191 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7105 (mt-10) REVERT: B 63 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 157 PHE cc_start: 0.6779 (p90) cc_final: 0.6301 (p90) REVERT: B 186 PHE cc_start: 0.6999 (m-10) cc_final: 0.6787 (m-10) REVERT: B 364 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7286 (t0) REVERT: B 1041 ASP cc_start: 0.7065 (t0) cc_final: 0.6759 (t0) REVERT: C 18 LEU cc_start: 0.0801 (OUTLIER) cc_final: 0.0490 (pp) REVERT: C 153 MET cc_start: 0.5131 (tmm) cc_final: 0.4853 (tpt) REVERT: C 712 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 1005 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7390 (tm-30) REVERT: G 94 TYR cc_start: 0.2444 (OUTLIER) cc_final: 0.1986 (t80) REVERT: G 103 MET cc_start: 0.5556 (tpp) cc_final: 0.5007 (tpp) REVERT: L 87 TYR cc_start: 0.6393 (m-80) cc_final: 0.6125 (m-80) outliers start: 66 outliers final: 44 residues processed: 213 average time/residue: 0.1640 time to fit residues: 59.9036 Evaluate side-chains 196 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 178 ASP 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 754 LEU Chi-restraints excluded: chain A residue 859 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 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 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 1001 LEU 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 79 PHE 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 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE 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 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE 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 J residue 5 THR 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: 0.9990 chunk 196 optimal weight: 3.9990 chunk 345 optimal weight: 0.0050 chunk 99 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 382 optimal weight: 20.0000 chunk 349 optimal weight: 3.9990 chunk 212 optimal weight: 0.0980 chunk 193 optimal weight: 9.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.099563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.080309 restraints weight = 161271.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078696 restraints weight = 150383.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.079096 restraints weight = 145849.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.079062 restraints weight = 121564.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.079422 restraints weight = 98254.041| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31389 Z= 0.134 Angle : 0.578 13.460 42758 Z= 0.291 Chirality : 0.043 0.285 4898 Planarity : 0.003 0.038 5468 Dihedral : 5.529 59.582 4765 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 1.61 % Allowed : 12.29 % Favored : 86.10 % 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: -1.21 (0.13), residues: 3846 helix: 1.16 (0.21), residues: 646 sheet: -0.90 (0.17), residues: 890 loop : -1.37 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.019 0.001 TYR B 200 PHE 0.020 0.001 PHE C 464 TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00297 (31317) covalent geometry : angle 0.56434 (42587) SS BOND : bond 0.00213 ( 45) SS BOND : angle 2.15317 ( 90) hydrogen bonds : bond 0.03440 ( 1019) hydrogen bonds : angle 5.57370 ( 2742) link_NAG-ASN : bond 0.00310 ( 27) link_NAG-ASN : angle 1.91063 ( 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 216 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.967 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: B 63 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (p) REVERT: B 157 PHE cc_start: 0.6446 (p90) cc_final: 0.6123 (p90) REVERT: B 202 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7892 (mtpt) REVERT: B 364 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7260 (t0) REVERT: B 1041 ASP cc_start: 0.7193 (t0) cc_final: 0.6961 (t0) REVERT: C 18 LEU cc_start: 0.1102 (OUTLIER) cc_final: 0.0750 (pp) REVERT: C 153 MET cc_start: 0.4803 (tmm) cc_final: 0.4544 (tpt) REVERT: C 1005 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7436 (tm-30) REVERT: G 94 TYR cc_start: 0.2798 (OUTLIER) cc_final: 0.2286 (t80) REVERT: G 103 MET cc_start: 0.5020 (tpp) cc_final: 0.4611 (tpp) REVERT: L 87 TYR cc_start: 0.6431 (m-80) cc_final: 0.6212 (m-80) REVERT: J 24 ARG cc_start: 0.7358 (tpp-160) cc_final: 0.7157 (tpp-160) outliers start: 54 outliers final: 43 residues processed: 204 average time/residue: 0.1700 time to fit residues: 59.5333 Evaluate side-chains 192 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET 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 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 489 TYR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 1001 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 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 131 CYS 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 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE 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 J residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 140 optimal weight: 0.3980 chunk 214 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 374 optimal weight: 30.0000 chunk 347 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.096914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.077196 restraints weight = 160868.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.074706 restraints weight = 157071.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075157 restraints weight = 125785.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075404 restraints weight = 99706.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075433 restraints weight = 94298.573| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31389 Z= 0.242 Angle : 0.687 15.439 42758 Z= 0.351 Chirality : 0.046 0.286 4898 Planarity : 0.004 0.041 5468 Dihedral : 6.097 58.495 4764 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.32 % Rotamer: Outliers : 2.00 % Allowed : 12.20 % Favored : 85.80 % 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: -1.49 (0.13), residues: 3846 helix: 0.68 (0.20), residues: 651 sheet: -0.99 (0.16), residues: 938 loop : -1.52 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 96 TYR 0.023 0.002 TYR A 170 PHE 0.019 0.002 PHE B 392 TRP 0.018 0.002 TRP C1102 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00535 (31317) covalent geometry : angle 0.67331 (42587) SS BOND : bond 0.00406 ( 45) SS BOND : angle 2.35645 ( 90) hydrogen bonds : bond 0.03978 ( 1019) hydrogen bonds : angle 5.99178 ( 2742) link_NAG-ASN : bond 0.00393 ( 27) link_NAG-ASN : angle 2.21645 ( 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 218 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6862 (mt-10) REVERT: B 63 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 157 PHE cc_start: 0.6855 (p90) cc_final: 0.6359 (p90) REVERT: B 291 CYS cc_start: 0.5179 (m) cc_final: 0.4971 (m) REVERT: B 364 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7600 (t0) REVERT: B 1041 ASP cc_start: 0.7136 (t0) cc_final: 0.6918 (t0) REVERT: C 18 LEU cc_start: 0.0945 (OUTLIER) cc_final: 0.0585 (pp) REVERT: C 153 MET cc_start: 0.5346 (tmm) cc_final: 0.5002 (tpt) REVERT: C 1005 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7415 (tm-30) REVERT: G 94 TYR cc_start: 0.2804 (OUTLIER) cc_final: 0.2409 (t80) REVERT: H 103 MET cc_start: 0.8688 (mmm) cc_final: 0.8349 (mpp) REVERT: L 49 TYR cc_start: 0.8240 (p90) cc_final: 0.8024 (p90) REVERT: J 24 ARG cc_start: 0.7184 (tpp-160) cc_final: 0.6980 (tpp-160) outliers start: 67 outliers final: 46 residues processed: 204 average time/residue: 0.1570 time to fit residues: 55.6626 Evaluate side-chains 186 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET 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 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 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 777 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 69 HIS 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 524 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET 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 1034 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 94 TYR 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 J residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 12 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 chunk 375 optimal weight: 0.0970 chunk 199 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN L 3 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.098894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079847 restraints weight = 159362.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078268 restraints weight = 177303.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.078728 restraints weight = 136175.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078793 restraints weight = 110026.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.078903 restraints weight = 96041.724| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 31389 Z= 0.111 Angle : 0.594 12.694 42758 Z= 0.299 Chirality : 0.043 0.241 4898 Planarity : 0.003 0.040 5468 Dihedral : 5.566 59.171 4764 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 1.22 % Allowed : 12.94 % Favored : 85.83 % 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: -1.20 (0.13), residues: 3846 helix: 1.07 (0.21), residues: 653 sheet: -0.85 (0.17), residues: 894 loop : -1.36 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 98 TYR 0.021 0.001 TYR A 170 PHE 0.020 0.001 PHE B 392 TRP 0.012 0.001 TRP C 886 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00244 (31317) covalent geometry : angle 0.58415 (42587) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.81869 ( 90) hydrogen bonds : bond 0.03391 ( 1019) hydrogen bonds : angle 5.58271 ( 2742) link_NAG-ASN : bond 0.00289 ( 27) link_NAG-ASN : angle 1.81174 ( 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 205 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.905 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 191 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6573 (mt-10) REVERT: A 697 MET cc_start: 0.7961 (mmm) cc_final: 0.7712 (mmm) REVERT: B 63 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8763 (p) REVERT: B 157 PHE cc_start: 0.6566 (p90) cc_final: 0.6128 (p90) REVERT: B 291 CYS cc_start: 0.5067 (m) cc_final: 0.4828 (m) REVERT: B 364 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 737 ASP cc_start: 0.7046 (p0) cc_final: 0.5723 (p0) REVERT: B 753 LEU cc_start: 0.8879 (tt) cc_final: 0.8607 (tt) REVERT: B 1041 ASP cc_start: 0.7084 (t0) cc_final: 0.6831 (t0) REVERT: C 18 LEU cc_start: 0.1367 (OUTLIER) cc_final: 0.0976 (pp) REVERT: C 725 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 740 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7107 (tmm) REVERT: C 780 GLU cc_start: 0.7923 (pt0) cc_final: 0.7576 (pt0) REVERT: C 1005 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7334 (tm-30) REVERT: G 94 TYR cc_start: 0.2875 (OUTLIER) cc_final: 0.2383 (t80) REVERT: G 103 MET cc_start: 0.4889 (tpp) cc_final: 0.4339 (tpp) REVERT: I 103 MET cc_start: 0.3322 (pmm) cc_final: -0.1024 (mmm) outliers start: 41 outliers final: 34 residues processed: 194 average time/residue: 0.1611 time to fit residues: 54.3530 Evaluate side-chains 187 residues out of total 3382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP 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 722 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 777 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 276 LEU Chi-restraints excluded: chain C residue 277 LEU 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 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 94 TYR 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 29 ILE Chi-restraints excluded: chain J residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 158 optimal weight: 5.9990 chunk 363 optimal weight: 30.0000 chunk 257 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 356 optimal weight: 40.0000 chunk 216 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** J 90 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.097081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.077335 restraints weight = 160927.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074899 restraints weight = 158858.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.075280 restraints weight = 151663.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075129 restraints weight = 134270.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075446 restraints weight = 108819.898| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31389 Z= 0.194 Angle : 0.633 12.987 42758 Z= 0.322 Chirality : 0.044 0.254 4898 Planarity : 0.004 0.039 5468 Dihedral : 5.791 58.271 4764 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 1.58 % Allowed : 13.09 % Favored : 85.33 % 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: 0.84 (0.20), residues: 652 sheet: -0.88 (0.16), residues: 914 loop : -1.43 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.018 0.002 TYR A 170 PHE 0.019 0.002 PHE B 392 TRP 0.016 0.001 TRP C 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00429 (31317) covalent geometry : angle 0.62233 (42587) SS BOND : bond 0.00407 ( 45) SS BOND : angle 1.86429 ( 90) hydrogen bonds : bond 0.03742 ( 1019) hydrogen bonds : angle 5.77340 ( 2742) link_NAG-ASN : bond 0.00300 ( 27) link_NAG-ASN : angle 1.98837 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4847.15 seconds wall clock time: 85 minutes 14.82 seconds (5114.82 seconds total)