Starting phenix.real_space_refine on Wed Jun 25 05:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_20545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_20545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_20545.map" model { file = "/net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_20545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q07_20545/06_2025/6q07_20545.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 7 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 7 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 7 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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 24 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: 16.74, per 1000 atoms: 0.58 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: 9.23 Conformation dependent library (CDL) restraints added in 3.4 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: 4.77 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: 13.99 Time building geometry restraints manager: 10.30 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: 18429 26.84 - 53.68: 423 53.68 - 80.52: 144 80.52 - 107.37: 120 107.37 - 134.21: 30 Dihedral angle restraints: 19146 sinusoidal: 9030 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 19143 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: 0.18 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 69.900 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.190 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 15.925 134.208 12537 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.019 0.005 TRP C1184 HIS 0.009 0.003 HIS B 264 PHE 0.049 0.006 PHE C 473 TYR 0.079 0.011 TYR B 184 ARG 0.012 0.002 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.03228 ( 51) link_NAG-ASN : angle 2.67054 ( 153) link_ALPHA1-6 : bond 0.06151 ( 6) link_ALPHA1-6 : angle 13.04478 ( 18) link_BETA1-4 : bond 0.06174 ( 48) link_BETA1-4 : angle 3.05338 ( 144) link_ALPHA1-2 : bond 0.06666 ( 6) link_ALPHA1-2 : angle 3.34806 ( 18) link_ALPHA1-3 : bond 0.06120 ( 15) link_ALPHA1-3 : angle 3.79058 ( 45) hydrogen bonds : bond 0.15185 ( 1157) hydrogen bonds : angle 7.72053 ( 3024) SS BOND : bond 0.04843 ( 51) SS BOND : angle 3.44448 ( 102) glycosidic custom : bond 0.06179 ( 3) glycosidic custom : angle 7.06196 ( 9) covalent geometry : bond 0.02534 (29316) covalent geometry : angle 2.02262 (39903) *********************** 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 : 2.781 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: 0.8769 (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: 0.7624 (t80) REVERT: B 1069 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.8135 (mtp85) REVERT: C 60 GLN cc_start: 0.6464 (mt0) cc_final: 0.6256 (mm-40) REVERT: C 650 CYS cc_start: 0.5744 (m) cc_final: 0.5401 (m) outliers start: 27 outliers final: 1 residues processed: 607 average time/residue: 1.5077 time to fit residues: 1083.8649 Evaluate side-chains 286 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 4.950 ------------------------------------------------------------------------------- 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: chunk 291 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 167 HIS A 280 GLN A 395 GLN A 521 ASN A 681 HIS A 708 GLN A 765 ASN 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 280 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 C1056 GLN C1072 ASN C1163 ASN C1208 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119659 restraints weight = 36303.680| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.89 r_work: 0.3259 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29496 Z= 0.200 Angle : 0.791 19.974 40392 Z= 0.388 Chirality : 0.053 1.216 4848 Planarity : 0.004 0.036 4971 Dihedral : 13.203 116.619 6509 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.56 % Allowed : 7.69 % Favored : 88.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3447 helix: 0.43 (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 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS C 348 PHE 0.024 0.002 PHE B 850 TYR 0.024 0.002 TYR A 909 ARG 0.005 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 51) link_NAG-ASN : angle 3.93371 ( 153) link_ALPHA1-6 : bond 0.00645 ( 6) link_ALPHA1-6 : angle 1.65415 ( 18) link_BETA1-4 : bond 0.00978 ( 48) link_BETA1-4 : angle 3.01889 ( 144) link_ALPHA1-2 : bond 0.00369 ( 6) link_ALPHA1-2 : angle 1.71718 ( 18) link_ALPHA1-3 : bond 0.00846 ( 15) link_ALPHA1-3 : angle 2.57723 ( 45) hydrogen bonds : bond 0.05305 ( 1157) hydrogen bonds : angle 6.26919 ( 3024) SS BOND : bond 0.00623 ( 51) SS BOND : angle 1.97787 ( 102) glycosidic custom : bond 0.00225 ( 3) glycosidic custom : angle 0.40299 ( 9) covalent geometry : bond 0.00442 (29316) covalent geometry : angle 0.72133 (39903) *********************** 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: 106 poor density : 353 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: A 344 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 402 LEU cc_start: 0.9090 (mt) cc_final: 0.8845 (mt) REVERT: A 488 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 665 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7866 (tttt) REVERT: A 666 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: A 854 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7351 (ttmm) REVERT: A 940 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6777 (p0) REVERT: A 1137 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (mtm) REVERT: B 219 TYR cc_start: 0.8314 (m-80) cc_final: 0.7999 (m-80) REVERT: B 402 LEU cc_start: 0.9157 (mt) cc_final: 0.8939 (mt) REVERT: B 488 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8000 (tp) REVERT: B 618 GLN cc_start: 0.7803 (mt0) cc_final: 0.7569 (mt0) REVERT: B 666 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: B 997 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8043 (mp) REVERT: B 1008 MET cc_start: 0.7503 (ptm) cc_final: 0.7262 (ptm) REVERT: B 1137 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: C 343 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7586 (p0) REVERT: C 666 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: C 841 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7476 (ttm-80) REVERT: C 1036 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8706 (mt) REVERT: C 1091 SER cc_start: 0.8725 (t) cc_final: 0.8355 (m) REVERT: C 1137 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (mtm) outliers start: 106 outliers final: 35 residues processed: 421 average time/residue: 1.2185 time to fit residues: 616.5370 Evaluate side-chains 314 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 3.141 ------------------------------------------------------------------------------- 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 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 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 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 974 GLN Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1036 LEU 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: chunk 312 optimal weight: 0.8980 chunk 201 optimal weight: 0.0370 chunk 205 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 319 optimal weight: 0.3980 chunk 215 optimal weight: 0.8980 chunk 251 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN B 346 GLN B 466 GLN B 501 ASN B 516 GLN B 647 ASN B 833 GLN C 466 GLN C 647 ASN C 842 GLN C 974 GLN C 981 ASN C1020 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117957 restraints weight = 36347.824| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.94 r_work: 0.3239 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29496 Z= 0.159 Angle : 0.682 15.532 40392 Z= 0.332 Chirality : 0.047 0.607 4848 Planarity : 0.004 0.041 4971 Dihedral : 10.672 94.479 6507 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.53 % Allowed : 10.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3447 helix: 0.76 (0.20), residues: 717 sheet: 0.42 (0.16), residues: 804 loop : 0.16 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 553 HIS 0.004 0.001 HIS C 167 PHE 0.016 0.001 PHE A 827 TYR 0.021 0.001 TYR A 909 ARG 0.004 0.000 ARG A 511 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 51) link_NAG-ASN : angle 2.97705 ( 153) link_ALPHA1-6 : bond 0.00784 ( 6) link_ALPHA1-6 : angle 1.40651 ( 18) link_BETA1-4 : bond 0.01011 ( 48) link_BETA1-4 : angle 2.62273 ( 144) link_ALPHA1-2 : bond 0.00531 ( 6) link_ALPHA1-2 : angle 1.61671 ( 18) link_ALPHA1-3 : bond 0.01173 ( 15) link_ALPHA1-3 : angle 1.32781 ( 45) hydrogen bonds : bond 0.04598 ( 1157) hydrogen bonds : angle 5.81568 ( 3024) SS BOND : bond 0.00502 ( 51) SS BOND : angle 1.90287 ( 102) glycosidic custom : bond 0.00255 ( 3) glycosidic custom : angle 0.66117 ( 9) covalent geometry : bond 0.00350 (29316) covalent geometry : angle 0.63118 (39903) *********************** 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 416 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 311 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.7483 (t) cc_final: 0.7145 (m) REVERT: A 219 TYR cc_start: 0.8317 (m-80) cc_final: 0.8098 (m-80) REVERT: A 343 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7391 (p0) REVERT: A 488 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8086 (tp) REVERT: A 576 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: A 758 ARG cc_start: 0.8392 (mtm180) cc_final: 0.8159 (mtm110) REVERT: A 803 THR cc_start: 0.9019 (p) cc_final: 0.8499 (t) REVERT: A 841 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7217 (tpt-90) REVERT: A 854 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7360 (ttmm) REVERT: A 960 TRP cc_start: 0.6475 (OUTLIER) cc_final: 0.5901 (t60) REVERT: A 1008 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7386 (ptm) REVERT: A 1035 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7774 (tttp) REVERT: A 1039 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 1137 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7987 (mtt) REVERT: B 251 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8622 (tp) REVERT: B 346 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7749 (tp-100) REVERT: B 369 LYS cc_start: 0.5149 (mptt) cc_final: 0.4826 (mptt) REVERT: B 402 LEU cc_start: 0.9157 (mt) cc_final: 0.8948 (mt) REVERT: B 502 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8637 (ttpp) REVERT: B 650 CYS cc_start: 0.7392 (p) cc_final: 0.7051 (p) REVERT: B 803 THR cc_start: 0.8997 (p) cc_final: 0.8527 (t) REVERT: B 854 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7471 (tptm) REVERT: B 943 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8453 (tpp) REVERT: B 997 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 1008 MET cc_start: 0.7553 (ptm) cc_final: 0.7334 (ptm) REVERT: B 1035 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7826 (tttp) REVERT: B 1055 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 1137 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: C 74 LEU cc_start: 0.9321 (mt) cc_final: 0.9112 (mt) REVERT: C 141 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7732 (mmm160) REVERT: C 219 TYR cc_start: 0.8348 (m-80) cc_final: 0.7862 (m-80) REVERT: C 576 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7484 (mp-120) REVERT: C 666 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: C 758 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7937 (mtm110) REVERT: C 841 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7311 (mtp-110) REVERT: C 842 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.6856 (mp-120) REVERT: C 854 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (tptm) REVERT: C 997 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 1036 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8938 (mt) REVERT: C 1055 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8680 (mt) REVERT: C 1091 SER cc_start: 0.8720 (t) cc_final: 0.8313 (m) REVERT: C 1137 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (mtt) REVERT: C 1142 TYR cc_start: 0.8816 (m-80) cc_final: 0.8457 (m-80) outliers start: 105 outliers final: 37 residues processed: 377 average time/residue: 1.1569 time to fit residues: 530.3896 Evaluate side-chains 325 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 343 ASP 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 576 GLN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1008 MET 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 1127 VAL 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 346 GLN Chi-restraints excluded: chain B residue 350 SER 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 667 THR 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 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 151 SER Chi-restraints excluded: chain C residue 202 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 620 CYS Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 854 LYS 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: chunk 129 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 305 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 516 GLN A 708 GLN A 836 HIS A 942 ASN A1208 GLN B 647 ASN B 681 HIS B 832 ASN C 261 GLN C 319 GLN C 647 ASN C 681 HIS C 942 ASN C 981 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116252 restraints weight = 36892.656| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.95 r_work: 0.3209 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29496 Z= 0.179 Angle : 0.650 10.258 40392 Z= 0.320 Chirality : 0.046 0.456 4848 Planarity : 0.004 0.040 4971 Dihedral : 9.126 88.672 6507 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.60 % Allowed : 10.85 % Favored : 85.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3447 helix: 0.88 (0.20), residues: 714 sheet: 0.20 (0.16), residues: 852 loop : 0.12 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 535 HIS 0.004 0.001 HIS C 348 PHE 0.018 0.002 PHE B 850 TYR 0.023 0.002 TYR A 909 ARG 0.004 0.000 ARG A1069 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 51) link_NAG-ASN : angle 2.71687 ( 153) link_ALPHA1-6 : bond 0.00942 ( 6) link_ALPHA1-6 : angle 1.31724 ( 18) link_BETA1-4 : bond 0.00814 ( 48) link_BETA1-4 : angle 2.31987 ( 144) link_ALPHA1-2 : bond 0.00365 ( 6) link_ALPHA1-2 : angle 1.62805 ( 18) link_ALPHA1-3 : bond 0.01104 ( 15) link_ALPHA1-3 : angle 1.73095 ( 45) hydrogen bonds : bond 0.04470 ( 1157) hydrogen bonds : angle 5.73543 ( 3024) SS BOND : bond 0.00553 ( 51) SS BOND : angle 1.92656 ( 102) glycosidic custom : bond 0.00356 ( 3) glycosidic custom : angle 0.64964 ( 9) covalent geometry : bond 0.00413 (29316) covalent geometry : angle 0.60456 (39903) *********************** 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 385 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 278 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7693 (mmm160) REVERT: A 343 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7414 (p0) REVERT: A 400 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: A 488 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 576 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: A 666 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: A 758 ARG cc_start: 0.8481 (mtm180) cc_final: 0.8247 (mtm110) REVERT: A 803 THR cc_start: 0.9031 (p) cc_final: 0.8543 (t) REVERT: A 830 LYS cc_start: 0.8426 (mmpt) cc_final: 0.7989 (mttm) REVERT: A 841 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7212 (tpt-90) REVERT: A 854 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7256 (ttmm) REVERT: A 960 TRP cc_start: 0.6489 (OUTLIER) cc_final: 0.5828 (t60) REVERT: A 1035 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7906 (tttp) REVERT: A 1137 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8189 (mtt) REVERT: A 1142 TYR cc_start: 0.8955 (m-80) cc_final: 0.8718 (m-80) REVERT: B 219 TYR cc_start: 0.8197 (m-80) cc_final: 0.7940 (m-80) REVERT: B 251 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8603 (tp) REVERT: B 369 LYS cc_start: 0.5229 (mptt) cc_final: 0.4840 (mptt) REVERT: B 502 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8615 (ttpp) REVERT: B 618 GLN cc_start: 0.8085 (mt0) cc_final: 0.7669 (mt0) REVERT: B 666 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: B 803 THR cc_start: 0.8986 (p) cc_final: 0.8532 (t) REVERT: B 854 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7515 (tptm) REVERT: B 943 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: B 997 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 1035 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7964 (tttp) REVERT: B 1137 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: C 74 LEU cc_start: 0.9328 (mt) cc_final: 0.9115 (mt) REVERT: C 141 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7793 (mmm160) REVERT: C 174 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7858 (t0) REVERT: C 219 TYR cc_start: 0.8343 (m-80) cc_final: 0.8115 (m-80) REVERT: C 666 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: C 854 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7601 (tptm) REVERT: C 997 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8259 (mt) REVERT: C 1035 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7771 (tttp) REVERT: C 1036 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9039 (mt) REVERT: C 1055 ILE cc_start: 0.8899 (mt) cc_final: 0.8691 (mt) REVERT: C 1091 SER cc_start: 0.8772 (t) cc_final: 0.8330 (m) REVERT: C 1137 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8254 (mtt) REVERT: C 1142 TYR cc_start: 0.8829 (m-80) cc_final: 0.8535 (m-80) outliers start: 107 outliers final: 39 residues processed: 348 average time/residue: 1.1795 time to fit residues: 494.7927 Evaluate side-chains 315 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 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 576 GLN Chi-restraints excluded: chain A residue 579 THR 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 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 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 299 SER 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 662 ILE Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 667 THR 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 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 960 TRP 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 1137 MET Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR 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 579 THR Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 848 ASN 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 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: chunk 214 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 192 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 107 GLN A 466 GLN A 942 ASN A1208 GLN B 346 GLN B 348 HIS B 647 ASN B1132 ASN C 98 GLN C 107 GLN C 348 HIS C 647 ASN C 681 HIS C 981 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111327 restraints weight = 36542.776| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.89 r_work: 0.3157 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 29496 Z= 0.267 Angle : 0.734 16.208 40392 Z= 0.361 Chirality : 0.048 0.343 4848 Planarity : 0.005 0.047 4971 Dihedral : 8.927 89.108 6507 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.37 % Allowed : 10.99 % Favored : 84.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3447 helix: 0.63 (0.20), residues: 714 sheet: 0.01 (0.16), residues: 873 loop : -0.05 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 535 HIS 0.007 0.001 HIS C 348 PHE 0.021 0.002 PHE B 850 TYR 0.021 0.002 TYR A 909 ARG 0.006 0.001 ARG C 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 51) link_NAG-ASN : angle 3.23684 ( 153) link_ALPHA1-6 : bond 0.00719 ( 6) link_ALPHA1-6 : angle 1.37759 ( 18) link_BETA1-4 : bond 0.00801 ( 48) link_BETA1-4 : angle 2.31120 ( 144) link_ALPHA1-2 : bond 0.00331 ( 6) link_ALPHA1-2 : angle 1.60130 ( 18) link_ALPHA1-3 : bond 0.01142 ( 15) link_ALPHA1-3 : angle 1.43827 ( 45) hydrogen bonds : bond 0.04971 ( 1157) hydrogen bonds : angle 5.88545 ( 3024) SS BOND : bond 0.00650 ( 51) SS BOND : angle 2.09942 ( 102) glycosidic custom : bond 0.00339 ( 3) glycosidic custom : angle 0.71449 ( 9) covalent geometry : bond 0.00637 (29316) covalent geometry : angle 0.68579 (39903) *********************** 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 417 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 287 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7646 (mmm160) REVERT: A 319 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: A 343 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7406 (p0) REVERT: A 400 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8099 (ttmm) REVERT: A 488 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7899 (tt) REVERT: A 576 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 666 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: A 758 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8225 (mtt90) REVERT: A 830 LYS cc_start: 0.8429 (mmpt) cc_final: 0.7986 (mttm) REVERT: A 841 ARG cc_start: 0.7433 (mtp180) cc_final: 0.7123 (tpt-90) REVERT: A 960 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.5232 (t60) REVERT: A 1035 LYS cc_start: 0.8278 (mtpp) cc_final: 0.8059 (tttp) REVERT: A 1137 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: A 1142 TYR cc_start: 0.8995 (m-80) cc_final: 0.8772 (m-80) REVERT: B 26 VAL cc_start: 0.8238 (m) cc_final: 0.7995 (p) REVERT: B 141 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7518 (mmm160) REVERT: B 219 TYR cc_start: 0.8398 (m-80) cc_final: 0.8123 (m-80) REVERT: B 369 LYS cc_start: 0.5313 (mptt) cc_final: 0.4981 (mptt) REVERT: B 666 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: B 909 TYR cc_start: 0.7212 (t80) cc_final: 0.7003 (t80) REVERT: B 943 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8531 (ttp) REVERT: B 960 TRP cc_start: 0.6832 (OUTLIER) cc_final: 0.6616 (t60) REVERT: B 995 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7960 (ttpt) REVERT: B 997 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 1008 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7712 (ptm) REVERT: B 1035 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8094 (tttp) REVERT: C 26 VAL cc_start: 0.8306 (m) cc_final: 0.8104 (p) REVERT: C 74 LEU cc_start: 0.9355 (mt) cc_final: 0.9151 (mt) REVERT: C 141 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7820 (mmm160) REVERT: C 174 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8005 (t0) REVERT: C 219 TYR cc_start: 0.8325 (m-80) cc_final: 0.8051 (m-80) REVERT: C 413 LYS cc_start: 0.8342 (tttp) cc_final: 0.8127 (tttm) REVERT: C 488 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8116 (tp) REVERT: C 666 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: C 854 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7609 (tptm) REVERT: C 997 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8307 (mt) REVERT: C 1035 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7943 (tttp) REVERT: C 1036 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9091 (mt) REVERT: C 1055 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8806 (mt) outliers start: 130 outliers final: 60 residues processed: 370 average time/residue: 1.4966 time to fit residues: 680.7109 Evaluate side-chains 342 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 3.235 ------------------------------------------------------------------------------- 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 319 GLN 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 722 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP 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 B residue 51 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 141 ARG 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 350 SER Chi-restraints excluded: chain B residue 355 ASP 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 666 GLU Chi-restraints excluded: chain B residue 667 THR 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 819 GLN Chi-restraints excluded: chain B residue 852 SER 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 974 GLN 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 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1168 VAL 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 151 SER 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 289 THR 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 465 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR 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 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 819 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 1035 LYS Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1055 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 200 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 331 optimal weight: 0.7980 chunk 309 optimal weight: 0.5980 chunk 208 optimal weight: 0.8980 chunk 148 optimal weight: 0.2980 chunk 188 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 681 HIS A1208 GLN B 346 GLN B 647 ASN B1160 ASN C 647 ASN C 681 HIS C 842 GLN C1160 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114130 restraints weight = 36590.432| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.96 r_work: 0.3184 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3708 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= 0.155 Angle : 0.629 13.964 40392 Z= 0.309 Chirality : 0.045 0.263 4848 Planarity : 0.004 0.043 4971 Dihedral : 8.130 87.941 6507 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.39 % Allowed : 13.07 % Favored : 83.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3447 helix: 0.92 (0.20), residues: 714 sheet: -0.06 (0.16), residues: 873 loop : 0.01 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 535 HIS 0.006 0.001 HIS C 681 PHE 0.016 0.001 PHE A 850 TYR 0.019 0.001 TYR B 649 ARG 0.006 0.000 ARG C 652 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 51) link_NAG-ASN : angle 2.70972 ( 153) link_ALPHA1-6 : bond 0.00887 ( 6) link_ALPHA1-6 : angle 1.48022 ( 18) link_BETA1-4 : bond 0.00770 ( 48) link_BETA1-4 : angle 2.26570 ( 144) link_ALPHA1-2 : bond 0.00356 ( 6) link_ALPHA1-2 : angle 1.63288 ( 18) link_ALPHA1-3 : bond 0.01080 ( 15) link_ALPHA1-3 : angle 1.50640 ( 45) hydrogen bonds : bond 0.04229 ( 1157) hydrogen bonds : angle 5.71527 ( 3024) SS BOND : bond 0.00517 ( 51) SS BOND : angle 1.89791 ( 102) glycosidic custom : bond 0.00462 ( 3) glycosidic custom : angle 0.94544 ( 9) covalent geometry : bond 0.00353 (29316) covalent geometry : angle 0.58306 (39903) *********************** 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 379 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 278 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7682 (mmm160) REVERT: A 343 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7506 (p0) REVERT: A 369 LYS cc_start: 0.5471 (mptt) cc_final: 0.4940 (mptt) REVERT: A 400 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8121 (ttmm) REVERT: A 488 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7953 (tt) REVERT: A 576 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 666 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: A 758 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8244 (mtt90) REVERT: A 803 THR cc_start: 0.9027 (p) cc_final: 0.8555 (t) REVERT: A 960 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5091 (t60) REVERT: A 1142 TYR cc_start: 0.8981 (m-80) cc_final: 0.8741 (m-80) REVERT: B 26 VAL cc_start: 0.8252 (m) cc_final: 0.8014 (p) REVERT: B 369 LYS cc_start: 0.5319 (mptt) cc_final: 0.5018 (mptt) REVERT: B 579 THR cc_start: 0.7152 (p) cc_final: 0.6945 (t) REVERT: B 666 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: B 803 THR cc_start: 0.9001 (p) cc_final: 0.8531 (t) REVERT: B 913 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6219 (mpt) REVERT: B 943 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: B 960 TRP cc_start: 0.6757 (OUTLIER) cc_final: 0.6552 (t60) REVERT: B 997 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (mt) REVERT: C 74 LEU cc_start: 0.9344 (mt) cc_final: 0.9128 (mt) REVERT: C 141 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7810 (mmm160) REVERT: C 174 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7873 (t0) REVERT: C 219 TYR cc_start: 0.8294 (m-80) cc_final: 0.8039 (m-80) REVERT: C 346 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7753 (tp-100) REVERT: C 576 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: C 666 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: C 803 THR cc_start: 0.9021 (p) cc_final: 0.8541 (t) REVERT: C 815 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8073 (tm-30) REVERT: C 854 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7629 (tptm) REVERT: C 997 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 1015 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7896 (p) REVERT: C 1035 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7890 (tttp) REVERT: C 1055 ILE cc_start: 0.8898 (mt) cc_final: 0.8697 (mt) REVERT: C 1142 TYR cc_start: 0.8854 (m-80) cc_final: 0.8604 (m-80) REVERT: C 1223 LEU cc_start: 0.8172 (mt) cc_final: 0.7963 (mp) outliers start: 101 outliers final: 40 residues processed: 346 average time/residue: 1.6106 time to fit residues: 678.8794 Evaluate side-chains 321 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 3.904 ------------------------------------------------------------------------------- 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 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 1086 LEU 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 299 SER Chi-restraints excluded: chain B residue 355 ASP 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 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 784 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 913 MET 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 1059 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1199 SER Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL 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 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 1035 LYS Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 68 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 229 optimal weight: 0.2980 chunk 237 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 323 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 681 HIS A1208 GLN B 346 GLN B 647 ASN C 60 GLN C 647 ASN C 681 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113534 restraints weight = 36724.921| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.86 r_work: 0.3187 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3829 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= 0.180 Angle : 0.655 14.089 40392 Z= 0.323 Chirality : 0.046 0.290 4848 Planarity : 0.004 0.045 4971 Dihedral : 7.943 87.433 6507 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.36 % Allowed : 13.47 % Favored : 83.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3447 helix: 0.92 (0.20), residues: 714 sheet: -0.03 (0.17), residues: 870 loop : -0.03 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 535 HIS 0.005 0.001 HIS B 681 PHE 0.017 0.001 PHE B 850 TYR 0.027 0.001 TYR C 649 ARG 0.004 0.000 ARG C 652 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 51) link_NAG-ASN : angle 2.64731 ( 153) link_ALPHA1-6 : bond 0.00842 ( 6) link_ALPHA1-6 : angle 1.45312 ( 18) link_BETA1-4 : bond 0.00754 ( 48) link_BETA1-4 : angle 2.16416 ( 144) link_ALPHA1-2 : bond 0.00353 ( 6) link_ALPHA1-2 : angle 1.60074 ( 18) link_ALPHA1-3 : bond 0.01041 ( 15) link_ALPHA1-3 : angle 1.43697 ( 45) hydrogen bonds : bond 0.04309 ( 1157) hydrogen bonds : angle 5.69573 ( 3024) SS BOND : bond 0.00678 ( 51) SS BOND : angle 2.44641 ( 102) glycosidic custom : bond 0.00397 ( 3) glycosidic custom : angle 0.87857 ( 9) covalent geometry : bond 0.00424 (29316) covalent geometry : angle 0.60872 (39903) *********************** 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 369 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 269 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7657 (mmm160) REVERT: A 343 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7708 (p0) REVERT: A 400 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8117 (ttmm) REVERT: A 488 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 576 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: A 666 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: A 803 THR cc_start: 0.9010 (p) cc_final: 0.8528 (t) REVERT: A 830 LYS cc_start: 0.8349 (mmpt) cc_final: 0.7951 (mttm) REVERT: A 960 TRP cc_start: 0.6714 (OUTLIER) cc_final: 0.5053 (t60) REVERT: A 1142 TYR cc_start: 0.8971 (m-80) cc_final: 0.8736 (m-80) REVERT: B 26 VAL cc_start: 0.8256 (m) cc_final: 0.8047 (p) REVERT: B 579 THR cc_start: 0.7233 (p) cc_final: 0.6980 (t) REVERT: B 666 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: B 803 THR cc_start: 0.8996 (p) cc_final: 0.8552 (t) REVERT: B 913 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6286 (mpt) REVERT: B 943 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: B 997 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8203 (mt) REVERT: C 74 LEU cc_start: 0.9342 (mt) cc_final: 0.9124 (mt) REVERT: C 141 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7795 (mmm160) REVERT: C 174 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7965 (t0) REVERT: C 219 TYR cc_start: 0.8287 (m-80) cc_final: 0.8043 (m-80) REVERT: C 576 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: C 666 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: C 803 THR cc_start: 0.9051 (p) cc_final: 0.8585 (t) REVERT: C 815 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8081 (tm-30) REVERT: C 854 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7587 (tptm) REVERT: C 997 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 1035 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7931 (tttp) REVERT: C 1142 TYR cc_start: 0.8879 (m-80) cc_final: 0.8652 (m-80) REVERT: C 1223 LEU cc_start: 0.8170 (mt) cc_final: 0.7967 (mp) outliers start: 100 outliers final: 49 residues processed: 342 average time/residue: 1.1737 time to fit residues: 489.4868 Evaluate side-chains 319 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 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 1086 LEU 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 299 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 355 ASP 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 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 819 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 913 MET 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 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 151 SER Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 202 THR 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 662 ILE Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 848 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 31 optimal weight: 0.4980 chunk 236 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 229 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 681 HIS A1208 GLN B 647 ASN C 280 GLN 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 = 0.3634 r_free = 0.3634 target = 0.140808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114891 restraints weight = 36625.812| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.85 r_work: 0.3205 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3928 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= 0.143 Angle : 0.629 15.640 40392 Z= 0.309 Chirality : 0.045 0.263 4848 Planarity : 0.004 0.045 4971 Dihedral : 7.525 86.771 6507 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.96 % Allowed : 14.38 % Favored : 82.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3447 helix: 1.01 (0.20), residues: 717 sheet: 0.01 (0.17), residues: 855 loop : -0.03 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 535 HIS 0.005 0.001 HIS B 681 PHE 0.015 0.001 PHE C 183 TYR 0.020 0.001 TYR A 649 ARG 0.004 0.000 ARG A1069 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 51) link_NAG-ASN : angle 2.61338 ( 153) link_ALPHA1-6 : bond 0.00904 ( 6) link_ALPHA1-6 : angle 1.49171 ( 18) link_BETA1-4 : bond 0.00752 ( 48) link_BETA1-4 : angle 2.03878 ( 144) link_ALPHA1-2 : bond 0.00385 ( 6) link_ALPHA1-2 : angle 1.59812 ( 18) link_ALPHA1-3 : bond 0.01006 ( 15) link_ALPHA1-3 : angle 1.45829 ( 45) hydrogen bonds : bond 0.04023 ( 1157) hydrogen bonds : angle 5.63524 ( 3024) SS BOND : bond 0.00755 ( 51) SS BOND : angle 2.37236 ( 102) glycosidic custom : bond 0.00473 ( 3) glycosidic custom : angle 0.96100 ( 9) covalent geometry : bond 0.00332 (29316) covalent geometry : angle 0.58335 (39903) *********************** 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 356 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 268 time to evaluate : 3.122 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: 0.7634 (mmm160) REVERT: A 343 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7691 (p0) REVERT: A 400 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8154 (ttmm) REVERT: A 576 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 579 THR cc_start: 0.7376 (p) cc_final: 0.7082 (t) REVERT: A 666 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: A 803 THR cc_start: 0.8957 (p) cc_final: 0.8544 (t) REVERT: A 815 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7639 (mp10) REVERT: A 960 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.4977 (t60) REVERT: A 1142 TYR cc_start: 0.8939 (m-80) cc_final: 0.8716 (m-80) REVERT: B 26 VAL cc_start: 0.8199 (m) cc_final: 0.7996 (p) REVERT: B 579 THR cc_start: 0.7247 (p) cc_final: 0.6979 (t) REVERT: B 614 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7815 (mtm110) REVERT: B 666 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: B 803 THR cc_start: 0.8975 (p) cc_final: 0.8562 (t) REVERT: B 815 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7606 (mp10) REVERT: B 891 GLU cc_start: 0.8512 (tt0) cc_final: 0.8227 (mt-10) REVERT: B 913 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6210 (mpt) REVERT: B 997 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (mt) REVERT: B 1055 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8474 (pt) REVERT: C 141 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7814 (mmm160) REVERT: C 219 TYR cc_start: 0.8254 (m-80) cc_final: 0.7986 (m-80) REVERT: C 346 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7632 (tp-100) REVERT: C 488 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8050 (tp) REVERT: C 576 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: C 666 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 803 THR cc_start: 0.9008 (p) cc_final: 0.8577 (t) REVERT: C 841 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7204 (tpt-90) REVERT: C 854 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7584 (tptm) REVERT: C 921 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7640 (mtp85) REVERT: C 997 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8274 (mt) REVERT: C 1035 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7990 (tttp) REVERT: C 1142 TYR cc_start: 0.8860 (m-80) cc_final: 0.8594 (m-80) REVERT: C 1223 LEU cc_start: 0.8150 (mt) cc_final: 0.7948 (mp) outliers start: 88 outliers final: 46 residues processed: 333 average time/residue: 1.1312 time to fit residues: 460.6077 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 : 2.884 ------------------------------------------------------------------------------- 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 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 724 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1086 LEU 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 350 SER Chi-restraints excluded: chain B residue 355 ASP 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 651 LEU 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 913 MET Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE 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 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 151 SER 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 557 SER Chi-restraints excluded: chain C residue 576 GLN 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 724 VAL Chi-restraints excluded: chain C residue 784 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 264 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 263 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A1208 GLN B 346 GLN B 647 ASN C 60 GLN 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 = 0.3622 r_free = 0.3622 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113818 restraints weight = 36551.826| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.85 r_work: 0.3189 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 29496 Z= 0.170 Angle : 0.643 15.674 40392 Z= 0.316 Chirality : 0.045 0.304 4848 Planarity : 0.004 0.046 4971 Dihedral : 7.407 86.839 6507 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3447 helix: 1.01 (0.20), residues: 717 sheet: 0.02 (0.17), residues: 849 loop : -0.09 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 535 HIS 0.003 0.001 HIS C 681 PHE 0.016 0.001 PHE B 850 TYR 0.019 0.001 TYR C 649 ARG 0.003 0.000 ARG C 652 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 51) link_NAG-ASN : angle 2.74705 ( 153) link_ALPHA1-6 : bond 0.00856 ( 6) link_ALPHA1-6 : angle 1.45688 ( 18) link_BETA1-4 : bond 0.00716 ( 48) link_BETA1-4 : angle 1.95684 ( 144) link_ALPHA1-2 : bond 0.00373 ( 6) link_ALPHA1-2 : angle 1.56621 ( 18) link_ALPHA1-3 : bond 0.00956 ( 15) link_ALPHA1-3 : angle 1.44752 ( 45) hydrogen bonds : bond 0.04168 ( 1157) hydrogen bonds : angle 5.64464 ( 3024) SS BOND : bond 0.00785 ( 51) SS BOND : angle 2.31026 ( 102) glycosidic custom : bond 0.00413 ( 3) glycosidic custom : angle 0.91834 ( 9) covalent geometry : bond 0.00400 (29316) covalent geometry : angle 0.59844 (39903) *********************** 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 349 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7631 (mmm160) REVERT: A 343 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7711 (p0) REVERT: A 400 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8176 (ttmm) REVERT: A 488 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 576 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 666 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: A 803 THR cc_start: 0.8990 (p) cc_final: 0.8574 (t) REVERT: A 960 TRP cc_start: 0.6711 (OUTLIER) cc_final: 0.4910 (t60) REVERT: A 1142 TYR cc_start: 0.8944 (m-80) cc_final: 0.8725 (m-80) REVERT: A 1160 ASN cc_start: 0.7743 (t0) cc_final: 0.7500 (t0) REVERT: B 26 VAL cc_start: 0.8238 (m) cc_final: 0.8028 (p) REVERT: B 579 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.7005 (t) REVERT: B 666 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: B 803 THR cc_start: 0.8986 (p) cc_final: 0.8577 (t) REVERT: B 815 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7599 (mp10) REVERT: B 891 GLU cc_start: 0.8539 (tt0) cc_final: 0.8278 (mt-10) REVERT: B 943 MET cc_start: 0.8763 (ttm) cc_final: 0.8523 (ttp) REVERT: B 997 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8189 (mt) REVERT: B 1055 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8419 (pt) REVERT: C 141 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7812 (mmm160) REVERT: C 219 TYR cc_start: 0.8275 (m-80) cc_final: 0.7994 (m-80) REVERT: C 346 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7684 (tp-100) REVERT: C 488 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 576 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: C 666 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 803 THR cc_start: 0.8999 (p) cc_final: 0.8572 (t) REVERT: C 854 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7588 (tptm) REVERT: C 921 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7663 (mtp85) REVERT: C 997 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 1035 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8025 (tttp) REVERT: C 1142 TYR cc_start: 0.8892 (m-80) cc_final: 0.8687 (m-80) outliers start: 87 outliers final: 49 residues processed: 323 average time/residue: 1.1502 time to fit residues: 457.0009 Evaluate side-chains 317 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 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 1086 LEU 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 350 SER Chi-restraints excluded: chain B residue 355 ASP 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 651 LEU 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 910 ASP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 997 ILE 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 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 151 SER 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 557 SER Chi-restraints excluded: chain C residue 576 GLN 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 724 VAL 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 1035 LYS Chi-restraints excluded: chain C residue 1059 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 138 optimal weight: 0.0060 chunk 188 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 343 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 98 optimal weight: 0.0010 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 681 HIS A1056 GLN A1208 GLN B 346 GLN B 647 ASN C 60 GLN C 647 ASN C 681 HIS C 733 GLN C1031 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115230 restraints weight = 36432.273| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.86 r_work: 0.3206 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29496 Z= 0.130 Angle : 0.628 20.917 40392 Z= 0.308 Chirality : 0.044 0.243 4848 Planarity : 0.004 0.045 4971 Dihedral : 7.170 86.152 6507 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.00 % Rotamer: Outliers : 2.28 % Allowed : 15.22 % Favored : 82.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3447 helix: 1.16 (0.20), residues: 717 sheet: 0.01 (0.17), residues: 849 loop : -0.08 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 535 HIS 0.003 0.001 HIS C 681 PHE 0.013 0.001 PHE B 850 TYR 0.037 0.001 TYR A 105 ARG 0.003 0.000 ARG C 652 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 51) link_NAG-ASN : angle 2.98808 ( 153) link_ALPHA1-6 : bond 0.00921 ( 6) link_ALPHA1-6 : angle 1.47165 ( 18) link_BETA1-4 : bond 0.00721 ( 48) link_BETA1-4 : angle 1.90131 ( 144) link_ALPHA1-2 : bond 0.00408 ( 6) link_ALPHA1-2 : angle 1.57903 ( 18) link_ALPHA1-3 : bond 0.00934 ( 15) link_ALPHA1-3 : angle 1.47636 ( 45) hydrogen bonds : bond 0.03881 ( 1157) hydrogen bonds : angle 5.56129 ( 3024) SS BOND : bond 0.00717 ( 51) SS BOND : angle 2.03286 ( 102) glycosidic custom : bond 0.00447 ( 3) glycosidic custom : angle 0.97203 ( 9) covalent geometry : bond 0.00295 (29316) covalent geometry : angle 0.58066 (39903) ********************** 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 326 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 400 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (ttmm) REVERT: A 576 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: A 579 THR cc_start: 0.7265 (p) cc_final: 0.6996 (t) REVERT: A 666 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: A 803 THR cc_start: 0.8957 (p) cc_final: 0.8566 (t) REVERT: A 815 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7640 (mp10) REVERT: A 960 TRP cc_start: 0.6759 (OUTLIER) cc_final: 0.4865 (t60) REVERT: A 1142 TYR cc_start: 0.8942 (m-80) cc_final: 0.8703 (m-80) REVERT: A 1160 ASN cc_start: 0.7765 (t0) cc_final: 0.7525 (t0) REVERT: B 409 TYR cc_start: 0.9138 (p90) cc_final: 0.8905 (p90) REVERT: B 579 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6973 (t) REVERT: B 666 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: B 803 THR cc_start: 0.8943 (p) cc_final: 0.8548 (t) REVERT: B 815 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7576 (mp10) REVERT: B 891 GLU cc_start: 0.8510 (tt0) cc_final: 0.8244 (mt-10) REVERT: B 913 MET cc_start: 0.7180 (mpp) cc_final: 0.6972 (mpt) REVERT: B 943 MET cc_start: 0.8765 (ttm) cc_final: 0.8540 (ttp) REVERT: B 997 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 1055 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8461 (pt) REVERT: C 141 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7810 (mmm160) REVERT: C 219 TYR cc_start: 0.8289 (m-80) cc_final: 0.8020 (m-80) REVERT: C 346 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7644 (tp-100) REVERT: C 488 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 576 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: C 666 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: C 803 THR cc_start: 0.8949 (p) cc_final: 0.8540 (t) REVERT: C 841 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7228 (ttm-80) REVERT: C 854 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7576 (tptm) REVERT: C 921 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7662 (mtp85) REVERT: C 997 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (mt) REVERT: C 1035 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8045 (tttp) REVERT: C 1142 TYR cc_start: 0.8855 (m-80) cc_final: 0.8645 (m-80) outliers start: 68 outliers final: 44 residues processed: 310 average time/residue: 1.1033 time to fit residues: 418.5818 Evaluate side-chains 307 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 662 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1086 LEU 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 299 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 355 ASP 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 651 LEU 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 965 SER Chi-restraints excluded: chain B residue 997 ILE 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 1199 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 151 SER 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 557 SER Chi-restraints excluded: chain C residue 576 GLN 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 724 VAL 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: chunk 215 optimal weight: 0.4980 chunk 307 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 241 optimal weight: 0.0970 chunk 262 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 202 optimal weight: 0.0030 chunk 339 optimal weight: 4.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 346 GLN B 647 ASN B 833 GLN 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 = 0.3644 r_free = 0.3644 target = 0.141706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115895 restraints weight = 36607.454| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.85 r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29496 Z= 0.128 Angle : 0.622 17.828 40392 Z= 0.305 Chirality : 0.044 0.238 4848 Planarity : 0.004 0.045 4971 Dihedral : 7.037 85.767 6507 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 2.39 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3447 helix: 1.19 (0.20), residues: 714 sheet: 0.08 (0.16), residues: 885 loop : -0.08 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 535 HIS 0.007 0.001 HIS B 348 PHE 0.014 0.001 PHE C 183 TYR 0.019 0.001 TYR C 64 ARG 0.003 0.000 ARG A1069 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 51) link_NAG-ASN : angle 2.86775 ( 153) link_ALPHA1-6 : bond 0.00927 ( 6) link_ALPHA1-6 : angle 1.45760 ( 18) link_BETA1-4 : bond 0.00718 ( 48) link_BETA1-4 : angle 1.86330 ( 144) link_ALPHA1-2 : bond 0.00417 ( 6) link_ALPHA1-2 : angle 1.57134 ( 18) link_ALPHA1-3 : bond 0.00909 ( 15) link_ALPHA1-3 : angle 1.48477 ( 45) hydrogen bonds : bond 0.03854 ( 1157) hydrogen bonds : angle 5.51329 ( 3024) SS BOND : bond 0.00695 ( 51) SS BOND : angle 2.14052 ( 102) glycosidic custom : bond 0.00512 ( 3) glycosidic custom : angle 0.98173 ( 9) covalent geometry : bond 0.00295 (29316) covalent geometry : angle 0.57502 (39903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19685.01 seconds wall clock time: 344 minutes 1.21 seconds (20641.21 seconds total)