Starting phenix.real_space_refine on Wed Oct 28 15:36:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6q07_20545/10_2026/6q07_20545.cif" } resolution = 2.9 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= 0.003 sd= 0.089 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 147 5.16 5 C 18108 2.51 5 N 4533 2.21 5 O 5949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28737 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "B" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "C" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'FOL': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'FOL': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'FOL': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 28737 At special positions: 0 Unit cell: (149.1, 156.45, 160.65, 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 147 16.00 O 5949 8.00 N 4533 7.00 C 18108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.08 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.09 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.06 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.12 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.09 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.05 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.08 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.01 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.17 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.09 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.02 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.06 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.12 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.09 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.05 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.08 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.09 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.02 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.06 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.12 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.09 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA J 3 " - " MAN J 5 " " BMA P 3 " - " MAN P 6 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " GAL M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " GAL W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " GAL g 2 " BETA2-6 " GAL M 2 " - " SIA M 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL W 2 " - " SIA W 3 " " GAL g 2 " - " SIA g 3 " NAG-ASN " NAG A1414 " - " ASN A 487 " " NAG A1415 " - " ASN A 592 " " NAG A1416 " - " ASN A 619 " " NAG A1417 " - " ASN A 719 " " NAG A1418 " - " ASN A 774 " " NAG A1419 " - " ASN A 785 " " NAG A1429 " - " ASN A 104 " " NAG A1435 " - " ASN A 155 " " NAG B1414 " - " ASN B 487 " " NAG B1415 " - " ASN B 592 " " NAG B1416 " - " ASN B 619 " " NAG B1417 " - " ASN B 719 " " NAG B1418 " - " ASN B 774 " " NAG B1419 " - " ASN B 785 " " NAG B1429 " - " ASN B 104 " " NAG B1435 " - " ASN B 155 " " NAG C1414 " - " ASN C 487 " " NAG C1415 " - " ASN C 592 " " NAG C1416 " - " ASN C 619 " " NAG C1417 " - " ASN C 719 " " NAG C1418 " - " ASN C 774 " " NAG C1419 " - " ASN C 785 " " NAG C1429 " - " ASN C 104 " " NAG C1435 " - " ASN C 155 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 236 " " NAG F 1 " - " ASN A 410 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN A 66 " " NAG J 1 " - " ASN A 125 " " NAG K 1 " - " ASN A 166 " " NAG L 1 " - " ASN A 244 " " NAG N 1 " - " ASN B 222 " " NAG O 1 " - " ASN B 236 " " NAG P 1 " - " ASN B 410 " " NAG Q 1 " - " ASN B 870 " " NAG R 1 " - " ASN B1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 125 " " NAG U 1 " - " ASN B 166 " " NAG V 1 " - " ASN B 244 " " NAG X 1 " - " ASN C 222 " " NAG Y 1 " - " ASN C 236 " " NAG Z 1 " - " ASN C 410 " " NAG a 1 " - " ASN C 870 " " NAG b 1 " - " ASN C1213 " " NAG c 1 " - " ASN C 66 " " NAG d 1 " - " ASN C 125 " " NAG e 1 " - " ASN C 166 " " NAG f 1 " - " ASN C 244 " Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1442 " pdb=" CB FOL B1442 " pdb=" CB FOL C1442 " Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 57 sheets defined 27.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.317A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 5.381A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 removed outlier: 3.918A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET B 913 " --> pdb=" O TYR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 953 Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.317A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.773A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.599A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.040A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 675 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.469A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 5.656A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 779 " --> pdb=" O ALA B 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.836A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.426A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 675 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.470A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1191 through 1195 removed outlier: 5.657A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY B1188 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.925A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE7, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.040A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.166A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF5, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.572A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.525A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AF8, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 3 1.07 - 1.26: 4514 1.26 - 1.46: 12261 1.46 - 1.66: 12322 1.66 - 1.86: 216 Bond restraints: 29316 Sorted by residual: bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.05e+02 bond pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.04e+02 bond pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.868 0.367 1.22e-02 6.72e+03 9.04e+02 bond pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.50e+02 bond pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 1.331 1.556 -0.226 1.43e-02 4.89e+03 2.49e+02 ... (remaining 29311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 38416 4.37 - 8.74: 1333 8.74 - 13.10: 100 13.10 - 17.47: 21 17.47 - 21.84: 33 Bond angle restraints: 39903 Sorted by residual: angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.33 -21.41 1.15e+00 7.56e-01 3.47e+02 angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.32 -21.40 1.15e+00 7.56e-01 3.46e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 120.92 142.29 -21.37 1.15e+00 7.56e-01 3.45e+02 angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 115.86 94.50 21.36 1.24e+00 6.50e-01 2.97e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 115.86 94.50 21.36 1.24e+00 6.50e-01 2.97e+02 ... (remaining 39898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 16062 26.84 - 53.68: 264 53.68 - 80.52: 81 80.52 - 107.37: 18 107.37 - 134.21: 3 Dihedral angle restraints: 16428 sinusoidal: 6312 harmonic: 10116 Sorted by residual: dihedral pdb=" N CYS C 383 " pdb=" C CYS C 383 " pdb=" CA CYS C 383 " pdb=" CB CYS C 383 " ideal model delta harmonic sigma weight residual 122.80 96.14 26.66 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" N CYS A 383 " pdb=" C CYS A 383 " pdb=" CA CYS A 383 " pdb=" CB CYS A 383 " ideal model delta harmonic sigma weight residual 122.80 96.16 26.64 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" N CYS B 383 " pdb=" C CYS B 383 " pdb=" CA CYS B 383 " pdb=" CB CYS B 383 " ideal model delta harmonic sigma weight residual 122.80 96.16 26.64 0 2.50e+00 1.60e-01 1.14e+02 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4771 0.390 - 0.780: 68 0.780 - 1.170: 6 1.170 - 1.560: 0 1.560 - 1.950: 3 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 MAN J 5 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 5 " pdb=" O5 MAN J 5 " both_signs ideal model delta sigma weight residual False 2.40 2.95 -0.55 2.00e-02 2.50e+03 7.57e+02 chirality pdb=" C1 MAN d 4 " pdb=" O3 BMA d 3 " pdb=" C2 MAN d 4 " pdb=" O5 MAN d 4 " both_signs ideal model delta sigma weight residual False 2.40 2.90 -0.50 2.00e-02 2.50e+03 6.33e+02 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.80 -0.40 2.00e-02 2.50e+03 4.07e+02 ... (remaining 4845 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 777 " 0.078 2.00e-02 2.50e+03 4.33e-02 3.74e+01 pdb=" CG TYR C 777 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 777 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 777 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR A 777 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 777 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.077 2.00e-02 2.50e+03 4.30e-02 3.70e+01 pdb=" CG TYR B 777 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " -0.070 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7409 2.78 - 3.31: 25909 3.31 - 3.84: 50980 3.84 - 4.37: 62164 4.37 - 4.90: 100486 Nonbonded interactions: 246948 Sorted by model distance: nonbonded pdb=" O5 BMA T 3 " pdb=" O6 BMA T 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA J 3 " pdb=" O6 BMA J 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA d 3 " pdb=" O6 BMA d 3 " model vdw 2.256 2.432 nonbonded pdb=" O ASP C 868 " pdb=" OD1 ASP C 868 " model vdw 2.311 3.040 nonbonded pdb=" O ASP A 868 " pdb=" OD1 ASP A 868 " model vdw 2.312 3.040 ... (remaining 246943 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'b' selection = chain 'e' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'c' selection = chain 'f' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'M' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'Q' and resid 1) selection = (chain 'W' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'a' and resid 1) selection = (chain 'g' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.230 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.026 0.367 29496 Z= 1.385 Angle : 2.059 26.697 40392 Z= 1.284 Chirality : 0.149 1.950 4848 Planarity : 0.009 0.047 4971 Dihedral : 11.598 134.208 9819 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.91 % Allowed : 1.31 % Favored : 97.78 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 3447 helix: -0.49 (0.17), residues: 678 sheet: 0.67 (0.17), residues: 846 loop : 0.79 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 190 TYR 0.079 0.011 TYR B 184 PHE 0.049 0.006 PHE C 473 TRP 0.019 0.005 TRP C1184 HIS 0.009 0.003 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.02534 / 1.38 (29316) covalent geometry : angle 2.02262 / 1.28 (39903) SS BOND : bond 0.04843 / 2.93 ( 51) SS BOND : angle 3.44448 / 2.26 ( 102) hydrogen bonds : bond 0.15185 / 9.98 ( 1157) hydrogen bonds : angle 7.72053 / 5.45 ( 3024) glycosidic custom : bond 0.06179 / 2.86 ( 3) glycosidic custom : angle 7.06196 / 3.94 ( 9) link_ALPHA1-2 : bond 0.06666 / 3.75 ( 6) link_ALPHA1-2 : angle 3.34806 / 2.14 ( 18) link_ALPHA1-3 : bond 0.06120 / 3.94 ( 15) link_ALPHA1-3 : angle 3.79058 / 2.29 ( 45) link_ALPHA1-6 : bond 0.06151 / 3.18 ( 6) link_ALPHA1-6 : angle 13.04478 / 8.09 ( 18) link_BETA1-4 : bond 0.06174 / 4.11 ( 48) link_BETA1-4 : angle 3.05338 / 2.09 ( 144) link_NAG-ASN : bond 0.03228 / 2.28 ( 51) link_NAG-ASN : angle 2.67054 / 1.81 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 592 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.9038 (mt) cc_final: 0.8768 (mt) REVERT: B 402 LEU cc_start: 0.9036 (mt) cc_final: 0.8809 (mt) REVERT: B 827 PHE cc_start: 0.7852 (t80) cc_final: 0.7626 (t80) REVERT: B 1069 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.8137 (mtp85) REVERT: C 60 GLN cc_start: 0.6464 (mt0) cc_final: 0.6259 (mm-40) REVERT: C 650 CYS cc_start: 0.5744 (m) cc_final: 0.5398 (m) outliers start: 27 outliers final: 1 residues processed: 607 average time/residue: 0.6031 time to fit residues: 433.3218 Evaluate side-chains 283 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 167 HIS A 261 GLN A 280 GLN A 395 GLN A 466 GLN A 521 ASN A 681 HIS A 708 GLN A 765 ASN A 836 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A 974 GLN A1063 GLN A1072 ASN A1163 ASN B 72 GLN B 107 GLN B 167 HIS B 280 GLN B 346 GLN B 395 GLN B 475 ASN B 521 ASN B 647 ASN B 765 ASN B 836 HIS B 942 ASN B1016 ASN B1063 GLN B1072 ASN B1208 GLN C 107 GLN C 167 HIS C 261 GLN C 280 GLN C 466 GLN C 501 ASN C 647 ASN C 826 GLN C 836 HIS ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 ASN C 974 GLN C1056 GLN C1072 ASN C1163 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118829 restraints weight = 36519.328| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.95 r_work: 0.3252 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29496 Z= 0.209 Angle : 0.781 19.675 40392 Z= 0.388 Chirality : 0.051 1.053 4848 Planarity : 0.004 0.035 4971 Dihedral : 6.399 116.610 3791 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.66 % Allowed : 7.69 % Favored : 88.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3447 helix: 0.42 (0.20), residues: 717 sheet: 0.44 (0.16), residues: 816 loop : 0.33 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 269 TYR 0.024 0.002 TYR A 909 PHE 0.025 0.002 PHE B 850 TRP 0.011 0.001 TRP A 960 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (29316) covalent geometry : angle 0.71826 / 0.37 (39903) SS BOND : bond 0.00537 / 0.32 ( 51) SS BOND : angle 2.08008 / 1.31 ( 102) hydrogen bonds : bond 0.05367 / 3.53 ( 1157) hydrogen bonds : angle 6.26903 / 4.41 ( 3024) glycosidic custom : bond 0.00408 / 0.20 ( 3) glycosidic custom : angle 0.52329 / 0.29 ( 9) link_ALPHA1-2 : bond 0.00376 / 0.21 ( 6) link_ALPHA1-2 : angle 1.59492 / 1.06 ( 18) link_ALPHA1-3 : bond 0.00495 / 0.32 ( 15) link_ALPHA1-3 : angle 1.49452 / 1.01 ( 45) link_ALPHA1-6 : bond 0.00509 / 0.29 ( 6) link_ALPHA1-6 : angle 1.41454 / 0.95 ( 18) link_BETA1-4 : bond 0.00880 / 0.60 ( 48) link_BETA1-4 : angle 2.77999 / 1.84 ( 144) link_NAG-ASN : bond 0.00758 / 0.53 ( 51) link_NAG-ASN : angle 3.86431 / 2.74 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 350 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: A 344 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 402 LEU cc_start: 0.9106 (mt) cc_final: 0.8859 (mt) REVERT: A 488 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 576 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 665 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7892 (tttt) REVERT: A 666 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: A 758 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7912 (mtt90) REVERT: A 854 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7346 (ttmm) REVERT: A 940 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6837 (p0) REVERT: A 1137 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8009 (mtm) REVERT: B 219 TYR cc_start: 0.8317 (m-80) cc_final: 0.8065 (m-80) REVERT: B 488 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8030 (tp) REVERT: B 618 GLN cc_start: 0.7853 (mt0) cc_final: 0.7630 (mt0) REVERT: B 666 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: B 997 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 1008 MET cc_start: 0.7517 (ptm) cc_final: 0.7276 (ptm) REVERT: B 1137 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8048 (mtt) REVERT: C 343 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7598 (p0) REVERT: C 666 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: C 841 ARG cc_start: 0.7717 (tpp-160) cc_final: 0.7482 (ttm-80) REVERT: C 1008 MET cc_start: 0.7691 (ptm) cc_final: 0.7480 (ptm) REVERT: C 1091 SER cc_start: 0.8720 (t) cc_final: 0.8351 (m) REVERT: C 1137 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7995 (mtm) outliers start: 109 outliers final: 36 residues processed: 421 average time/residue: 0.5479 time to fit residues: 278.0838 Evaluate side-chains 316 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 819 GLN Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [129, 141, 316, 26, 88, 0, 321, 240, 313, 44, 193] chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 321 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 313 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 ASN A 708 GLN A 927 GLN B 346 GLN B 466 GLN B 501 ASN B 516 GLN B 647 ASN C 647 ASN C 981 ASN C1020 GLN C1208 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115566 restraints weight = 36680.921| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.92 r_work: 0.3203 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29496 Z= 0.209 Angle : 0.710 12.021 40392 Z= 0.351 Chirality : 0.047 0.621 4848 Planarity : 0.004 0.040 4971 Dihedral : 5.803 95.245 3789 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.97 % Allowed : 9.68 % Favored : 86.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3447 helix: 0.65 (0.20), residues: 717 sheet: 0.31 (0.16), residues: 834 loop : 0.12 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 511 TYR 0.023 0.002 TYR A 909 PHE 0.019 0.002 PHE B 850 TRP 0.008 0.001 TRP C 553 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (29316) covalent geometry : angle 0.66293 / 0.34 (39903) SS BOND : bond 0.00671 / 0.39 ( 51) SS BOND : angle 2.09719 / 1.28 ( 102) hydrogen bonds : bond 0.04944 / 3.26 ( 1157) hydrogen bonds : angle 5.89891 / 4.16 ( 3024) glycosidic custom : bond 0.00520 / 0.23 ( 3) glycosidic custom : angle 0.87404 / 0.51 ( 9) link_ALPHA1-2 : bond 0.00436 / 0.25 ( 6) link_ALPHA1-2 : angle 1.54650 / 1.01 ( 18) link_ALPHA1-3 : bond 0.00562 / 0.37 ( 15) link_ALPHA1-3 : angle 1.30638 / 0.88 ( 45) link_ALPHA1-6 : bond 0.00474 / 0.28 ( 6) link_ALPHA1-6 : angle 1.52339 / 1.02 ( 18) link_BETA1-4 : bond 0.00925 / 0.63 ( 48) link_BETA1-4 : angle 2.57912 / 1.72 ( 144) link_NAG-ASN : bond 0.00721 / 0.55 ( 51) link_NAG-ASN : angle 2.85698 / 2.04 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 300 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7752 (mmm160) REVERT: A 343 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7391 (p0) REVERT: A 344 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 488 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 576 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 830 LYS cc_start: 0.8487 (mmpt) cc_final: 0.8037 (mttm) REVERT: A 841 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7164 (tpt-90) REVERT: A 854 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7425 (ttmm) REVERT: A 960 TRP cc_start: 0.6539 (OUTLIER) cc_final: 0.5893 (t60) REVERT: A 1008 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7416 (ptm) REVERT: A 1035 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7812 (tttp) REVERT: A 1039 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 1137 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: B 219 TYR cc_start: 0.8346 (m-80) cc_final: 0.8142 (m-80) REVERT: B 369 LYS cc_start: 0.5237 (mptt) cc_final: 0.4915 (mptt) REVERT: B 488 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8074 (tp) REVERT: B 502 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (ttpp) REVERT: B 650 CYS cc_start: 0.7481 (p) cc_final: 0.7088 (p) REVERT: B 665 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7754 (tttt) REVERT: B 854 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7517 (tptm) REVERT: B 997 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 1035 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7880 (tttp) REVERT: B 1055 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8675 (mt) REVERT: B 1137 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8119 (mtt) REVERT: C 74 LEU cc_start: 0.9336 (mt) cc_final: 0.9122 (mt) REVERT: C 141 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7732 (mmm160) REVERT: C 219 TYR cc_start: 0.8367 (m-80) cc_final: 0.7918 (m-80) REVERT: C 666 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: C 841 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7391 (mtp-110) REVERT: C 854 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7674 (tptm) REVERT: C 943 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8426 (ttp) REVERT: C 997 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8256 (mt) REVERT: C 1036 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8962 (mt) REVERT: C 1055 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 1091 SER cc_start: 0.8768 (t) cc_final: 0.8337 (m) REVERT: C 1137 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8250 (mtt) outliers start: 118 outliers final: 44 residues processed: 380 average time/residue: 0.5267 time to fit residues: 242.3661 Evaluate side-chains 330 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 819 GLN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1137 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [156, 248, 186, 89, 164, 151, 106, 228, 96, 78, 326] chunk 156 optimal weight: 0.8980 chunk 248 optimal weight: 0.0040 chunk 186 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 228 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 942 ASN B 346 GLN B 647 ASN B 832 ASN C 319 GLN C 647 ASN C 681 HIS C 942 ASN C 981 ASN C1208 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116290 restraints weight = 36687.251| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.89 r_work: 0.3213 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29496 Z= 0.153 Angle : 0.633 9.710 40392 Z= 0.311 Chirality : 0.045 0.337 4848 Planarity : 0.004 0.041 4971 Dihedral : 5.320 76.323 3789 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.60 % Allowed : 10.79 % Favored : 85.62 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3447 helix: 0.89 (0.20), residues: 717 sheet: 0.21 (0.16), residues: 840 loop : 0.09 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.025 0.001 TYR B 909 PHE 0.016 0.001 PHE A 183 TRP 0.007 0.001 TRP C 535 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (29316) covalent geometry : angle 0.58945 / 0.30 (39903) SS BOND : bond 0.00647 / 0.38 ( 51) SS BOND : angle 1.75872 / 1.09 ( 102) hydrogen bonds : bond 0.04328 / 2.86 ( 1157) hydrogen bonds : angle 5.71737 / 4.03 ( 3024) glycosidic custom : bond 0.00621 / 0.28 ( 3) glycosidic custom : angle 1.10349 / 0.66 ( 9) link_ALPHA1-2 : bond 0.00361 / 0.21 ( 6) link_ALPHA1-2 : angle 1.52837 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00534 / 0.34 ( 15) link_ALPHA1-3 : angle 1.30199 / 0.87 ( 45) link_ALPHA1-6 : bond 0.00451 / 0.26 ( 6) link_ALPHA1-6 : angle 1.39516 / 0.92 ( 18) link_BETA1-4 : bond 0.00854 / 0.59 ( 48) link_BETA1-4 : angle 2.20297 / 1.46 ( 144) link_NAG-ASN : bond 0.00579 / 0.43 ( 51) link_NAG-ASN : angle 2.70424 / 1.98 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 290 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7673 (mmm160) REVERT: A 343 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7417 (p0) REVERT: A 400 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8039 (ttmm) REVERT: A 402 LEU cc_start: 0.9175 (mt) cc_final: 0.8914 (mt) REVERT: A 488 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8019 (tp) REVERT: A 576 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: A 666 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: A 758 ARG cc_start: 0.8440 (mtm180) cc_final: 0.8194 (mtm110) REVERT: A 803 THR cc_start: 0.8966 (p) cc_final: 0.8480 (t) REVERT: A 841 ARG cc_start: 0.7445 (mtp180) cc_final: 0.7234 (tpt-90) REVERT: A 854 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7222 (ttmm) REVERT: A 960 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.4896 (t60) REVERT: A 1035 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7909 (tttp) REVERT: A 1137 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: B 251 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8582 (tp) REVERT: B 369 LYS cc_start: 0.5255 (mptt) cc_final: 0.4929 (mptt) REVERT: B 488 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 502 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (ttpp) REVERT: B 618 GLN cc_start: 0.8069 (mt0) cc_final: 0.7619 (mt0) REVERT: B 666 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: B 803 THR cc_start: 0.9040 (p) cc_final: 0.8596 (t) REVERT: B 854 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7470 (tptm) REVERT: B 997 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 1035 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8003 (tttp) REVERT: B 1137 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: C 74 LEU cc_start: 0.9331 (mt) cc_final: 0.9127 (mt) REVERT: C 141 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7780 (mmm160) REVERT: C 174 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7813 (t0) REVERT: C 219 TYR cc_start: 0.8322 (m-80) cc_final: 0.8083 (m-80) REVERT: C 576 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: C 666 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: C 803 THR cc_start: 0.9002 (p) cc_final: 0.8520 (t) REVERT: C 854 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7594 (tptm) REVERT: C 943 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: C 997 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8246 (mt) REVERT: C 1035 LYS cc_start: 0.8231 (mmmm) cc_final: 0.8006 (tttp) REVERT: C 1036 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8976 (mt) REVERT: C 1055 ILE cc_start: 0.8892 (mt) cc_final: 0.8660 (mt) REVERT: C 1091 SER cc_start: 0.8794 (t) cc_final: 0.8352 (m) REVERT: C 1137 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8283 (mtt) outliers start: 107 outliers final: 36 residues processed: 358 average time/residue: 0.5416 time to fit residues: 234.1064 Evaluate side-chains 318 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1137 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [100, 243, 94, 41, 260, 304, 144, 342, 200, 142, 229] chunk 100 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 260 optimal weight: 0.6980 chunk 304 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 229 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 942 ASN A1208 GLN B 346 GLN B 647 ASN C 107 GLN C 647 ASN C 681 HIS C 942 ASN C 981 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115504 restraints weight = 36672.204| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.91 r_work: 0.3200 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29496 Z= 0.161 Angle : 0.623 14.998 40392 Z= 0.306 Chirality : 0.044 0.250 4848 Planarity : 0.004 0.043 4971 Dihedral : 5.054 60.944 3789 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.76 % Allowed : 11.73 % Favored : 84.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3447 helix: 0.99 (0.20), residues: 717 sheet: 0.06 (0.16), residues: 897 loop : 0.08 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 841 TYR 0.017 0.001 TYR C 64 PHE 0.015 0.001 PHE B 850 TRP 0.007 0.001 TRP C 535 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (29316) covalent geometry : angle 0.58261 / 0.30 (39903) SS BOND : bond 0.00513 / 0.31 ( 51) SS BOND : angle 1.62099 / 1.01 ( 102) hydrogen bonds : bond 0.04271 / 2.82 ( 1157) hydrogen bonds : angle 5.64050 / 3.98 ( 3024) glycosidic custom : bond 0.00651 / 0.30 ( 3) glycosidic custom : angle 1.22987 / 0.71 ( 9) link_ALPHA1-2 : bond 0.00364 / 0.20 ( 6) link_ALPHA1-2 : angle 1.51323 / 0.98 ( 18) link_ALPHA1-3 : bond 0.00567 / 0.37 ( 15) link_ALPHA1-3 : angle 1.29222 / 0.87 ( 45) link_ALPHA1-6 : bond 0.00414 / 0.24 ( 6) link_ALPHA1-6 : angle 1.38297 / 0.91 ( 18) link_BETA1-4 : bond 0.00837 / 0.58 ( 48) link_BETA1-4 : angle 2.14713 / 1.43 ( 144) link_NAG-ASN : bond 0.00480 / 0.36 ( 51) link_NAG-ASN : angle 2.57869 / 1.84 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 282 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7694 (mmm160) REVERT: A 343 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7398 (p0) REVERT: A 400 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8094 (ttmm) REVERT: A 488 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7928 (tt) REVERT: A 576 GLN cc_start: 0.7617 (mt0) cc_final: 0.7290 (mp10) REVERT: A 666 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: A 758 ARG cc_start: 0.8484 (mtm180) cc_final: 0.8236 (mtt90) REVERT: A 803 THR cc_start: 0.9050 (p) cc_final: 0.8603 (t) REVERT: A 913 MET cc_start: 0.6654 (mpp) cc_final: 0.6430 (mtt) REVERT: A 958 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7876 (m) REVERT: A 960 TRP cc_start: 0.6637 (OUTLIER) cc_final: 0.5010 (t60) REVERT: A 1137 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: B 251 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8608 (tp) REVERT: B 346 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7674 (tp-100) REVERT: B 369 LYS cc_start: 0.5170 (mptt) cc_final: 0.4840 (mptt) REVERT: B 488 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8034 (tt) REVERT: B 502 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8629 (ttpp) REVERT: B 666 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: B 803 THR cc_start: 0.9032 (p) cc_final: 0.8584 (t) REVERT: B 854 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (tptm) REVERT: B 909 TYR cc_start: 0.7097 (t80) cc_final: 0.6867 (t80) REVERT: B 997 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 1008 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7642 (ptm) REVERT: B 1035 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8016 (tttp) REVERT: B 1055 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8579 (mt) REVERT: B 1137 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: C 74 LEU cc_start: 0.9335 (mt) cc_final: 0.9120 (mt) REVERT: C 141 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7784 (mmm160) REVERT: C 174 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7870 (t0) REVERT: C 219 TYR cc_start: 0.8298 (m-80) cc_final: 0.8038 (m-80) REVERT: C 666 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: C 803 THR cc_start: 0.8967 (p) cc_final: 0.8517 (t) REVERT: C 815 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7983 (tm-30) REVERT: C 854 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7577 (tptm) REVERT: C 943 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8443 (ttp) REVERT: C 997 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 1035 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7981 (tttp) REVERT: C 1036 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8992 (mt) REVERT: C 1055 ILE cc_start: 0.8909 (mt) cc_final: 0.8691 (mt) REVERT: C 1091 SER cc_start: 0.8714 (t) cc_final: 0.8354 (m) REVERT: C 1142 TYR cc_start: 0.8835 (m-80) cc_final: 0.8559 (m-80) REVERT: C 1223 LEU cc_start: 0.8122 (mt) cc_final: 0.7886 (mp) outliers start: 112 outliers final: 51 residues processed: 352 average time/residue: 0.5225 time to fit residues: 223.9422 Evaluate side-chains 328 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1036 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [252, 11, 330, 340, 295, 229, 55, 293, 44, 344, 96] chunk 252 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 340 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 344 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 681 HIS A 708 GLN A1208 GLN B 647 ASN B1160 ASN C 647 ASN C 681 HIS C 942 ASN C 981 ASN C1160 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115044 restraints weight = 36706.295| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.96 r_work: 0.3200 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29496 Z= 0.150 Angle : 0.612 14.198 40392 Z= 0.303 Chirality : 0.044 0.256 4848 Planarity : 0.004 0.043 4971 Dihedral : 4.915 52.690 3789 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.73 % Allowed : 12.67 % Favored : 83.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3447 helix: 1.00 (0.20), residues: 717 sheet: 0.04 (0.16), residues: 897 loop : 0.07 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1069 TYR 0.017 0.001 TYR C 64 PHE 0.016 0.001 PHE B 827 TRP 0.006 0.001 TRP C 535 HIS 0.006 0.001 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (29316) covalent geometry : angle 0.57099 / 0.29 (39903) SS BOND : bond 0.00496 / 0.30 ( 51) SS BOND : angle 2.01780 / 1.24 ( 102) hydrogen bonds : bond 0.04152 / 2.75 ( 1157) hydrogen bonds : angle 5.59413 / 3.94 ( 3024) glycosidic custom : bond 0.00681 / 0.31 ( 3) glycosidic custom : angle 1.35460 / 0.78 ( 9) link_ALPHA1-2 : bond 0.00367 / 0.21 ( 6) link_ALPHA1-2 : angle 1.51026 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00551 / 0.36 ( 15) link_ALPHA1-3 : angle 1.30488 / 0.88 ( 45) link_ALPHA1-6 : bond 0.00439 / 0.25 ( 6) link_ALPHA1-6 : angle 1.39555 / 0.92 ( 18) link_BETA1-4 : bond 0.00806 / 0.56 ( 48) link_BETA1-4 : angle 2.19305 / 1.46 ( 144) link_NAG-ASN : bond 0.00580 / 0.43 ( 51) link_NAG-ASN : angle 2.32974 / 1.69 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 273 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7709 (mmm160) REVERT: A 343 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 400 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (ttmm) REVERT: A 402 LEU cc_start: 0.9214 (mt) cc_final: 0.8948 (mt) REVERT: A 488 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 576 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: A 666 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: A 758 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8232 (mtt90) REVERT: A 803 THR cc_start: 0.9016 (p) cc_final: 0.8573 (t) REVERT: A 960 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.5013 (t60) REVERT: A 1137 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8335 (mtt) REVERT: A 1185 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8971 (t) REVERT: B 251 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 346 GLN cc_start: 0.8138 (mt0) cc_final: 0.7786 (OUTLIER) REVERT: B 369 LYS cc_start: 0.5300 (mptt) cc_final: 0.4985 (mptt) REVERT: B 488 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7991 (tt) REVERT: B 502 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (ttpp) REVERT: B 666 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: B 803 THR cc_start: 0.8967 (p) cc_final: 0.8505 (t) REVERT: B 997 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 1008 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (ptm) REVERT: B 1035 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.8023 (tttp) REVERT: B 1062 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: B 1137 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: C 74 LEU cc_start: 0.9324 (mt) cc_final: 0.9113 (mt) REVERT: C 141 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7807 (mmm160) REVERT: C 219 TYR cc_start: 0.8300 (m-80) cc_final: 0.8024 (m-80) REVERT: C 488 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8055 (tp) REVERT: C 576 GLN cc_start: 0.7478 (mp10) cc_final: 0.7197 (mp10) REVERT: C 666 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 803 THR cc_start: 0.8970 (p) cc_final: 0.8541 (t) REVERT: C 815 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8020 (tm-30) REVERT: C 854 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7605 (tptm) REVERT: C 943 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8414 (ttp) REVERT: C 997 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 1035 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7927 (tttp) REVERT: C 1036 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9011 (mt) REVERT: C 1055 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8693 (mt) REVERT: C 1091 SER cc_start: 0.8806 (t) cc_final: 0.8407 (m) REVERT: C 1142 TYR cc_start: 0.8822 (m-80) cc_final: 0.8566 (m-80) REVERT: C 1223 LEU cc_start: 0.8131 (mt) cc_final: 0.7915 (mp) outliers start: 111 outliers final: 54 residues processed: 349 average time/residue: 0.5090 time to fit residues: 215.9852 Evaluate side-chains 335 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1185 SER Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1055 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [263, 266, 27, 238, 91, 177, 68, 311, 243, 333, 118] chunk 263 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 333 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 HIS A 927 GLN A1208 GLN B 98 GLN B 346 GLN B 348 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 98 GLN C 348 HIS C 647 ASN C 681 HIS C 981 ASN C1160 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112138 restraints weight = 36714.704| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.86 r_work: 0.3162 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 29496 Z= 0.234 Angle : 0.701 14.680 40392 Z= 0.346 Chirality : 0.047 0.272 4848 Planarity : 0.005 0.045 4971 Dihedral : 5.186 43.441 3789 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.13 % Allowed : 12.50 % Favored : 83.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3447 helix: 0.77 (0.20), residues: 717 sheet: 0.03 (0.17), residues: 855 loop : -0.11 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 652 TYR 0.030 0.002 TYR C 649 PHE 0.019 0.002 PHE B 850 TRP 0.010 0.001 TRP B 960 HIS 0.005 0.001 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (29316) covalent geometry : angle 0.65972 / 0.34 (39903) SS BOND : bond 0.00685 / 0.45 ( 51) SS BOND : angle 2.43799 / 1.59 ( 102) hydrogen bonds : bond 0.04667 / 3.09 ( 1157) hydrogen bonds : angle 5.79575 / 4.10 ( 3024) glycosidic custom : bond 0.00682 / 0.31 ( 3) glycosidic custom : angle 1.40013 / 0.80 ( 9) link_ALPHA1-2 : bond 0.00304 / 0.18 ( 6) link_ALPHA1-2 : angle 1.50511 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00552 / 0.36 ( 15) link_ALPHA1-3 : angle 1.31714 / 0.89 ( 45) link_ALPHA1-6 : bond 0.00401 / 0.23 ( 6) link_ALPHA1-6 : angle 1.45622 / 0.96 ( 18) link_BETA1-4 : bond 0.00810 / 0.57 ( 48) link_BETA1-4 : angle 2.20115 / 1.46 ( 144) link_NAG-ASN : bond 0.00550 / 0.40 ( 51) link_NAG-ASN : angle 2.52652 / 1.82 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 268 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7616 (mmm160) REVERT: A 343 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7509 (p0) REVERT: A 400 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8085 (ttmm) REVERT: A 488 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 576 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 666 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: A 803 THR cc_start: 0.9031 (p) cc_final: 0.8570 (t) REVERT: A 830 LYS cc_start: 0.8480 (mmpt) cc_final: 0.8026 (mttm) REVERT: A 960 TRP cc_start: 0.6773 (OUTLIER) cc_final: 0.5204 (t60) REVERT: A 1137 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: B 26 VAL cc_start: 0.8266 (m) cc_final: 0.8053 (p) REVERT: B 409 TYR cc_start: 0.9192 (p90) cc_final: 0.8924 (p90) REVERT: B 488 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7991 (tt) REVERT: B 666 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 815 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7640 (mp10) REVERT: B 841 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: B 995 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7940 (ttpt) REVERT: B 997 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 1008 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7793 (ptm) REVERT: B 1035 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8029 (tttp) REVERT: C 74 LEU cc_start: 0.9336 (mt) cc_final: 0.9127 (mt) REVERT: C 141 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7812 (mmm160) REVERT: C 219 TYR cc_start: 0.8312 (m-80) cc_final: 0.8083 (m-80) REVERT: C 488 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 666 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: C 854 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7604 (tptm) REVERT: C 943 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8447 (ttp) REVERT: C 997 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (mt) REVERT: C 1035 LYS cc_start: 0.8282 (mmmm) cc_final: 0.8076 (tttp) REVERT: C 1036 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9046 (mt) REVERT: C 1055 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8819 (mt) REVERT: C 1091 SER cc_start: 0.8809 (t) cc_final: 0.8434 (m) outliers start: 123 outliers final: 62 residues processed: 354 average time/residue: 0.5081 time to fit residues: 219.0278 Evaluate side-chains 339 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 254 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1185 SER Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 995 LYS Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 827 PHE Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1055 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [40, 196, 164, 172, 312, 314, 240, 228, 68, 37, 43] chunk 40 optimal weight: 0.6980 chunk 196 optimal weight: 0.0060 chunk 164 optimal weight: 0.2980 chunk 172 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 348 HIS A1208 GLN B 346 GLN B 647 ASN C 647 ASN C 681 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114903 restraints weight = 36713.256| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.86 r_work: 0.3205 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29496 Z= 0.138 Angle : 0.634 21.076 40392 Z= 0.309 Chirality : 0.044 0.316 4848 Planarity : 0.004 0.044 4971 Dihedral : 4.868 35.287 3789 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.23 % Allowed : 13.74 % Favored : 83.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3447 helix: 1.03 (0.20), residues: 717 sheet: -0.07 (0.16), residues: 879 loop : -0.06 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 652 TYR 0.018 0.001 TYR C 64 PHE 0.019 0.001 PHE A 590 TRP 0.009 0.001 TRP A 535 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (29316) covalent geometry : angle 0.58244 / 0.30 (39903) SS BOND : bond 0.00714 / 0.45 ( 51) SS BOND : angle 2.29817 / 1.49 ( 102) hydrogen bonds : bond 0.04030 / 2.67 ( 1157) hydrogen bonds : angle 5.65642 / 3.99 ( 3024) glycosidic custom : bond 0.00810 / 0.37 ( 3) glycosidic custom : angle 1.63025 / 0.94 ( 9) link_ALPHA1-2 : bond 0.00381 / 0.21 ( 6) link_ALPHA1-2 : angle 1.52239 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00580 / 0.37 ( 15) link_ALPHA1-3 : angle 1.31354 / 0.88 ( 45) link_ALPHA1-6 : bond 0.00449 / 0.25 ( 6) link_ALPHA1-6 : angle 1.38412 / 0.91 ( 18) link_BETA1-4 : bond 0.00799 / 0.55 ( 48) link_BETA1-4 : angle 2.04686 / 1.36 ( 144) link_NAG-ASN : bond 0.00559 / 0.41 ( 51) link_NAG-ASN : angle 2.99550 / 2.13 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 270 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7691 (p0) REVERT: A 400 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8097 (ttmm) REVERT: A 488 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7758 (tt) REVERT: A 576 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: A 666 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: A 803 THR cc_start: 0.9021 (p) cc_final: 0.8598 (t) REVERT: A 960 TRP cc_start: 0.6743 (OUTLIER) cc_final: 0.5008 (t60) REVERT: A 1185 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9011 (t) REVERT: B 26 VAL cc_start: 0.8198 (m) cc_final: 0.7988 (p) REVERT: B 409 TYR cc_start: 0.9159 (p90) cc_final: 0.8893 (p90) REVERT: B 488 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 579 THR cc_start: 0.7116 (p) cc_final: 0.6865 (t) REVERT: B 666 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: B 803 THR cc_start: 0.8958 (p) cc_final: 0.8516 (t) REVERT: B 815 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7585 (mp10) REVERT: B 891 GLU cc_start: 0.8515 (tt0) cc_final: 0.8226 (mt-10) REVERT: B 997 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (mt) REVERT: B 1035 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (tttp) REVERT: C 60 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: C 74 LEU cc_start: 0.9346 (mt) cc_final: 0.9131 (mt) REVERT: C 141 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7796 (mmm160) REVERT: C 219 TYR cc_start: 0.8275 (m-80) cc_final: 0.7999 (m-80) REVERT: C 346 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7670 (tp-100) REVERT: C 413 LYS cc_start: 0.8372 (tttp) cc_final: 0.8163 (tttm) REVERT: C 488 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7990 (tp) REVERT: C 666 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: C 803 THR cc_start: 0.8972 (p) cc_final: 0.8547 (t) REVERT: C 815 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8006 (tm-30) REVERT: C 842 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: C 854 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7576 (tptm) REVERT: C 921 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7613 (mtp85) REVERT: C 997 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 1008 MET cc_start: 0.7477 (ptm) cc_final: 0.7267 (ptm) REVERT: C 1015 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7854 (p) REVERT: C 1035 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7960 (tttp) REVERT: C 1055 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 1091 SER cc_start: 0.8783 (t) cc_final: 0.8427 (m) outliers start: 96 outliers final: 44 residues processed: 337 average time/residue: 0.5164 time to fit residues: 212.2117 Evaluate side-chains 319 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1185 SER Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1055 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [142, 302, 155, 25, 57, 165, 255, 328, 249, 40, 203] chunk 142 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 328 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 107 GLN A 681 HIS B 346 GLN B 647 ASN C 647 ASN C 681 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112954 restraints weight = 36763.476| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.86 r_work: 0.3175 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29496 Z= 0.204 Angle : 0.667 16.073 40392 Z= 0.329 Chirality : 0.045 0.264 4848 Planarity : 0.004 0.046 4971 Dihedral : 4.951 38.164 3789 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.02 % Allowed : 14.21 % Favored : 82.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3447 helix: 0.87 (0.20), residues: 717 sheet: -0.08 (0.17), residues: 879 loop : -0.11 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 335 TYR 0.026 0.002 TYR B 909 PHE 0.018 0.002 PHE A 827 TRP 0.008 0.001 TRP C 535 HIS 0.007 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (29316) covalent geometry : angle 0.62439 / 0.32 (39903) SS BOND : bond 0.00847 / 0.52 ( 51) SS BOND : angle 2.62057 / 1.61 ( 102) hydrogen bonds : bond 0.04360 / 2.89 ( 1157) hydrogen bonds : angle 5.68602 / 4.01 ( 3024) glycosidic custom : bond 0.00709 / 0.32 ( 3) glycosidic custom : angle 1.62886 / 0.94 ( 9) link_ALPHA1-2 : bond 0.00319 / 0.18 ( 6) link_ALPHA1-2 : angle 1.50260 / 0.98 ( 18) link_ALPHA1-3 : bond 0.00568 / 0.37 ( 15) link_ALPHA1-3 : angle 1.30442 / 0.88 ( 45) link_ALPHA1-6 : bond 0.00393 / 0.22 ( 6) link_ALPHA1-6 : angle 1.43754 / 0.95 ( 18) link_BETA1-4 : bond 0.00774 / 0.54 ( 48) link_BETA1-4 : angle 2.04442 / 1.36 ( 144) link_NAG-ASN : bond 0.00509 / 0.37 ( 51) link_NAG-ASN : angle 2.50130 / 1.79 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 253 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7654 (mmm160) REVERT: A 343 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7685 (p0) REVERT: A 400 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: A 576 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 666 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: A 803 THR cc_start: 0.9007 (p) cc_final: 0.8556 (t) REVERT: A 830 LYS cc_start: 0.8418 (mmpt) cc_final: 0.7948 (mttm) REVERT: A 960 TRP cc_start: 0.6741 (OUTLIER) cc_final: 0.5077 (t60) REVERT: A 1185 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.9030 (t) REVERT: B 26 VAL cc_start: 0.8256 (m) cc_final: 0.8050 (p) REVERT: B 148 MET cc_start: 0.8922 (ttm) cc_final: 0.8701 (ttt) REVERT: B 346 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7657 (tp-100) REVERT: B 488 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8017 (tt) REVERT: B 579 THR cc_start: 0.7188 (p) cc_final: 0.6956 (t) REVERT: B 666 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: B 803 THR cc_start: 0.8995 (p) cc_final: 0.8548 (t) REVERT: B 815 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7608 (mp10) REVERT: B 891 GLU cc_start: 0.8545 (tt0) cc_final: 0.8277 (mt-10) REVERT: B 997 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 1035 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8052 (tttp) REVERT: C 74 LEU cc_start: 0.9347 (mt) cc_final: 0.9145 (mt) REVERT: C 141 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7814 (mmm160) REVERT: C 219 TYR cc_start: 0.8302 (m-80) cc_final: 0.8041 (m-80) REVERT: C 346 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7674 (tp-100) REVERT: C 413 LYS cc_start: 0.8385 (tttp) cc_final: 0.8180 (tttm) REVERT: C 488 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7877 (tp) REVERT: C 666 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: C 803 THR cc_start: 0.9017 (p) cc_final: 0.8583 (t) REVERT: C 815 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8046 (tm-30) REVERT: C 854 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7599 (tptm) REVERT: C 921 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7646 (mtp85) REVERT: C 997 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8272 (mt) REVERT: C 1035 LYS cc_start: 0.8239 (mmmm) cc_final: 0.8024 (tttp) REVERT: C 1055 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8809 (mt) REVERT: C 1091 SER cc_start: 0.8817 (t) cc_final: 0.8440 (m) REVERT: C 1223 LEU cc_start: 0.8189 (mt) cc_final: 0.7966 (mp) outliers start: 90 outliers final: 50 residues processed: 320 average time/residue: 0.5177 time to fit residues: 202.1823 Evaluate side-chains 317 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1185 SER Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 827 PHE Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1055 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [234, 114, 143, 325, 111, 335, 246, 74, 127, 16, 120] chunk 234 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 335 optimal weight: 0.8980 chunk 246 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 681 HIS A1056 GLN B 346 GLN B 647 ASN C 647 ASN C 681 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113970 restraints weight = 36548.613| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.85 r_work: 0.3189 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29496 Z= 0.160 Angle : 0.633 15.594 40392 Z= 0.313 Chirality : 0.044 0.254 4848 Planarity : 0.004 0.046 4971 Dihedral : 4.852 35.563 3789 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.55 % Allowed : 14.92 % Favored : 82.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3447 helix: 0.96 (0.20), residues: 714 sheet: -0.07 (0.17), residues: 879 loop : -0.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 652 TYR 0.019 0.001 TYR C 64 PHE 0.016 0.001 PHE B 850 TRP 0.009 0.001 TRP A 535 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (29316) covalent geometry : angle 0.59178 / 0.30 (39903) SS BOND : bond 0.00783 / 0.48 ( 51) SS BOND : angle 2.35628 / 1.47 ( 102) hydrogen bonds : bond 0.04127 / 2.74 ( 1157) hydrogen bonds : angle 5.62481 / 3.97 ( 3024) glycosidic custom : bond 0.00867 / 0.39 ( 3) glycosidic custom : angle 1.71348 / 0.99 ( 9) link_ALPHA1-2 : bond 0.00349 / 0.20 ( 6) link_ALPHA1-2 : angle 1.51047 / 0.98 ( 18) link_ALPHA1-3 : bond 0.00576 / 0.37 ( 15) link_ALPHA1-3 : angle 1.31227 / 0.89 ( 45) link_ALPHA1-6 : bond 0.00435 / 0.24 ( 6) link_ALPHA1-6 : angle 1.40016 / 0.92 ( 18) link_BETA1-4 : bond 0.00769 / 0.53 ( 48) link_BETA1-4 : angle 1.99485 / 1.33 ( 144) link_NAG-ASN : bond 0.00509 / 0.37 ( 51) link_NAG-ASN : angle 2.42182 / 1.73 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 258 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7647 (mmm160) REVERT: A 343 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7692 (p0) REVERT: A 400 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 576 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 666 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: A 803 THR cc_start: 0.8966 (p) cc_final: 0.8536 (t) REVERT: A 907 GLN cc_start: 0.8143 (pt0) cc_final: 0.7839 (mt0) REVERT: A 960 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.5024 (t60) REVERT: A 1160 ASN cc_start: 0.7736 (t0) cc_final: 0.7495 (t0) REVERT: A 1185 SER cc_start: 0.9355 (OUTLIER) cc_final: 0.9034 (t) REVERT: B 148 MET cc_start: 0.8905 (ttm) cc_final: 0.8690 (ttt) REVERT: B 488 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (tt) REVERT: B 579 THR cc_start: 0.7124 (p) cc_final: 0.6909 (t) REVERT: B 666 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: B 803 THR cc_start: 0.8954 (p) cc_final: 0.8519 (t) REVERT: B 815 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7596 (mp10) REVERT: B 891 GLU cc_start: 0.8529 (tt0) cc_final: 0.8303 (mt-10) REVERT: B 997 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 1035 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8055 (tttp) REVERT: C 74 LEU cc_start: 0.9346 (mt) cc_final: 0.9136 (mt) REVERT: C 141 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7802 (mmm160) REVERT: C 219 TYR cc_start: 0.8262 (m-80) cc_final: 0.7983 (m-80) REVERT: C 346 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7679 (tp-100) REVERT: C 413 LYS cc_start: 0.8380 (tttp) cc_final: 0.8176 (tttm) REVERT: C 488 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7919 (tp) REVERT: C 666 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: C 803 THR cc_start: 0.9001 (p) cc_final: 0.8563 (t) REVERT: C 815 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8046 (tm-30) REVERT: C 854 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7607 (tptm) REVERT: C 921 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7641 (mtp85) REVERT: C 997 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8270 (mt) REVERT: C 1035 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8076 (tttp) REVERT: C 1091 SER cc_start: 0.8790 (t) cc_final: 0.8409 (m) REVERT: C 1223 LEU cc_start: 0.8191 (mt) cc_final: 0.7983 (mp) outliers start: 76 outliers final: 46 residues processed: 314 average time/residue: 0.5083 time to fit residues: 195.5478 Evaluate side-chains 316 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1185 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1035 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: [57, 45, 124, 269, 306, 197, 194, 132, 60, 44, 204] chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.0050 chunk 124 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 306 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 681 HIS B 60 GLN B 346 GLN B 647 ASN C 647 ASN C 681 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115983 restraints weight = 36623.202| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.95 r_work: 0.3226 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29496 Z= 0.153 Angle : 0.624 15.411 40392 Z= 0.308 Chirality : 0.044 0.294 4848 Planarity : 0.004 0.046 4971 Dihedral : 4.765 32.918 3789 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 14.99 % Favored : 82.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3447 helix: 1.00 (0.20), residues: 714 sheet: -0.07 (0.17), residues: 879 loop : -0.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 652 TYR 0.028 0.001 TYR B 909 PHE 0.015 0.001 PHE B 850 TRP 0.009 0.001 TRP A 535 HIS 0.009 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (29316) covalent geometry : angle 0.58277 / 0.30 (39903) SS BOND : bond 0.00755 / 0.46 ( 51) SS BOND : angle 2.21060 / 1.39 ( 102) hydrogen bonds : bond 0.04039 / 2.68 ( 1157) hydrogen bonds : angle 5.56664 / 3.93 ( 3024) glycosidic custom : bond 0.00837 / 0.38 ( 3) glycosidic custom : angle 1.75101 / 1.01 ( 9) link_ALPHA1-2 : bond 0.00352 / 0.20 ( 6) link_ALPHA1-2 : angle 1.50598 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00580 / 0.37 ( 15) link_ALPHA1-3 : angle 1.31001 / 0.89 ( 45) link_ALPHA1-6 : bond 0.00452 / 0.25 ( 6) link_ALPHA1-6 : angle 1.39647 / 0.92 ( 18) link_BETA1-4 : bond 0.00763 / 0.53 ( 48) link_BETA1-4 : angle 1.92668 / 1.29 ( 144) link_NAG-ASN : bond 0.00482 / 0.35 ( 51) link_NAG-ASN : angle 2.52355 / 1.81 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9022.79 seconds wall clock time: 154 minutes 44.46 seconds (9284.46 seconds total)