Starting phenix.real_space_refine on Fri Mar 6 07:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.map" model { file = "/net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q05_20543/03_2026/6q05_20543.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.116 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 18168 2.51 5 N 4536 2.21 5 O 6126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28977 Number of models: 1 Model: "" Number of chains: 42 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: 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: "K" 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: "L" 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: "M" 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: "N" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: "a" 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: "b" 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: "c" 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: "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: 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: 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: "h" 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Unusual residues: {'FOL': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Time building chain proxies: 6.42, per 1000 atoms: 0.22 Number of scatterers: 28977 At special positions: 0 Unit cell: (151.2, 158.55, 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 6126 8.00 N 4536 7.00 C 18168 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=2.03 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 Q 4 " - " MAN Q 5 " " MAN Q 6 " - " MAN Q 7 " " MAN b 4 " - " MAN b 5 " " MAN b 6 " - " MAN b 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 6 " " BMA g 3 " - " MAN g 5 " " BMA h 3 " - " MAN h 5 " BETA1-3 " NAG N 1 " - " FUC N 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Y 1 " - " FUC Y 4 " " NAG j 1 " - " FUC j 4 " 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " GAL N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " GAL Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 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 " - " GAL j 2 " BETA2-3 " GAL N 2 " - " SIA N 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL Y 2 " - " SIA Y 3 " " GAL j 2 " - " SIA j 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 A1436 " - " 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 B1436 " - " 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 C1436 " - " 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 104 " " NAG K 1 " - " ASN A 125 " " NAG L 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 244 " " NAG O 1 " - " ASN B 222 " " NAG P 1 " - " ASN B 236 " " NAG Q 1 " - " ASN B 410 " " NAG R 1 " - " ASN B 870 " " NAG S 1 " - " ASN B1213 " " NAG T 1 " - " ASN B 66 " " NAG U 1 " - " ASN B 104 " " NAG V 1 " - " ASN B 125 " " NAG W 1 " - " ASN B 166 " " NAG X 1 " - " ASN B 244 " " NAG Z 1 " - " ASN C 222 " " NAG a 1 " - " ASN C 236 " " NAG b 1 " - " ASN C 410 " " NAG c 1 " - " ASN C 870 " " NAG d 1 " - " ASN C1213 " " NAG e 1 " - " ASN C 66 " " NAG f 1 " - " ASN C 104 " " NAG g 1 " - " ASN C 125 " " NAG h 1 " - " ASN C 166 " " NAG i 1 " - " ASN C 244 " Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 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 A1444 " pdb=" CB FOL B1444 " pdb=" CB FOL C1444 " Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 57 sheets defined 27.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 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: 4.149A 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: 3.788A 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: 3.918A 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: 3.679A 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: 4.318A 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: 4.149A 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: 3.788A 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: 5.380A 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: 4.318A 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: 3.855A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.148A 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: 3.788A 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: 3.918A 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: 4.174A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.086A 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: 6.614A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.759A 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: 4.164A 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: 5.243A 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: 6.513A 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: 5.424A 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: 4.862A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.933A 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: 5.362A 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: 5.438A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.717A 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: 6.628A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.732A 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: 5.657A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.835A 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: 5.825A 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: 4.609A 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: 4.748A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.657A 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: 4.164A 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: 5.244A 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: 6.294A 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: 4.449A 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: 5.424A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.724A 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: 5.933A 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: 6.276A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.362A 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: 6.628A 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: 5.469A 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: 5.656A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B1188 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.835A 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: 5.926A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.825A 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: 4.609A 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: 5.243A 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: 7.167A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.363A 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: 6.513A 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: 4.449A 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: 5.424A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.726A 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: 4.571A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.933A 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: 3.524A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.275A 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: 5.438A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.717A 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: 6.236A 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: 8.732A 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: 5.925A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.826A 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: 4.609A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 3 1.06 - 1.26: 4512 1.26 - 1.46: 12164 1.46 - 1.66: 12526 1.66 - 1.85: 216 Bond restraints: 29421 Sorted by residual: bond pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 1.234 0.866 0.368 1.22e-02 6.72e+03 9.12e+02 bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.866 0.368 1.22e-02 6.72e+03 9.11e+02 bond pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.09e+02 bond pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 1.331 1.558 -0.227 1.43e-02 4.89e+03 2.53e+02 bond pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 1.331 1.558 -0.227 1.43e-02 4.89e+03 2.52e+02 ... (remaining 29416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.72: 39789 7.72 - 15.43: 210 15.43 - 23.15: 45 23.15 - 30.86: 0 30.86 - 38.58: 3 Bond angle restraints: 40047 Sorted by residual: angle pdb=" N ASN B 199 " pdb=" CA ASN B 199 " pdb=" C ASN B 199 " ideal model delta sigma weight residual 111.07 149.65 -38.58 1.07e+00 8.73e-01 1.30e+03 angle pdb=" N ASN A 199 " pdb=" CA ASN A 199 " pdb=" C ASN A 199 " ideal model delta sigma weight residual 111.07 149.63 -38.56 1.07e+00 8.73e-01 1.30e+03 angle pdb=" N ASN C 199 " pdb=" CA ASN C 199 " pdb=" C ASN C 199 " ideal model delta sigma weight residual 111.07 149.59 -38.52 1.07e+00 8.73e-01 1.30e+03 angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.33 -21.41 1.15e+00 7.56e-01 3.46e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.30 -21.38 1.15e+00 7.56e-01 3.46e+02 ... (remaining 40042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 18607 26.83 - 53.66: 419 53.66 - 80.50: 138 80.50 - 107.33: 120 107.33 - 134.16: 33 Dihedral angle restraints: 19317 sinusoidal: 9201 harmonic: 10116 Sorted by residual: dihedral pdb=" N ASN A 199 " pdb=" C ASN A 199 " pdb=" CA ASN A 199 " pdb=" CB ASN A 199 " ideal model delta harmonic sigma weight residual 122.80 153.67 -30.87 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CA ASN B 199 " pdb=" CB ASN B 199 " ideal model delta harmonic sigma weight residual 122.80 153.67 -30.87 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N ASN C 199 " pdb=" C ASN C 199 " pdb=" CA ASN C 199 " pdb=" CB ASN C 199 " ideal model delta harmonic sigma weight residual 122.80 153.61 -30.81 0 2.50e+00 1.60e-01 1.52e+02 ... (remaining 19314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4813 0.390 - 0.780: 68 0.780 - 1.170: 6 1.170 - 1.560: 0 1.560 - 1.950: 6 Chirality restraints: 4893 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 3.01 -0.61 2.00e-02 2.50e+03 9.34e+02 chirality pdb=" C1 MAN g 4 " pdb=" O3 BMA g 3 " pdb=" C2 MAN g 4 " pdb=" O5 MAN g 4 " both_signs ideal model delta sigma weight residual False 2.40 2.80 -0.40 2.00e-02 2.50e+03 4.00e+02 chirality pdb=" C1 MAN V 5 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 5 " pdb=" O5 MAN V 5 " both_signs ideal model delta sigma weight residual False 2.40 2.78 -0.38 2.00e-02 2.50e+03 3.57e+02 ... (remaining 4890 not shown) Planarity restraints: 5025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR B 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 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 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.010 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 C 777 " 0.078 2.00e-02 2.50e+03 4.32e-02 3.73e+01 pdb=" CG TYR C 777 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 777 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 777 " -0.031 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 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5022 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7452 2.78 - 3.31: 26257 3.31 - 3.84: 51803 3.84 - 4.37: 63451 4.37 - 4.90: 101928 Nonbonded interactions: 250891 Sorted by model distance: nonbonded pdb=" O5 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.255 2.432 nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.255 2.432 nonbonded pdb=" O5 BMA g 3 " pdb=" O6 BMA g 3 " model vdw 2.255 2.432 nonbonded pdb=" NE2 GLN B 304 " pdb=" O6 NAG Y 1 " model vdw 2.277 3.120 nonbonded pdb=" NE2 GLN C 304 " pdb=" O6 NAG j 1 " model vdw 2.277 3.120 ... (remaining 250886 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'N' 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 'O' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'Y' 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 'Z' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'j' 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 'E' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'i' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'c' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'V' selection = chain 'W' selection = chain 'g' selection = chain 'h' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 28.580 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 0.368 29610 Z= 1.381 Angle : 2.099 38.578 40563 Z= 1.328 Chirality : 0.156 1.950 4893 Planarity : 0.009 0.048 4974 Dihedral : 15.796 134.160 12708 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.91 % Allowed : 1.41 % Favored : 97.68 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 3447 helix: -0.49 (0.17), residues: 678 sheet: 0.67 (0.17), residues: 846 loop : 0.78 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 190 TYR 0.079 0.011 TYR A 184 PHE 0.050 0.006 PHE B 473 TRP 0.019 0.005 TRP A1184 HIS 0.009 0.003 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.02528 (29421) covalent geometry : angle 2.06383 (40047) SS BOND : bond 0.04844 ( 51) SS BOND : angle 3.44205 ( 102) hydrogen bonds : bond 0.15185 ( 1157) hydrogen bonds : angle 7.71918 ( 3024) link_ALPHA1-2 : bond 0.06711 ( 6) link_ALPHA1-2 : angle 3.34600 ( 18) link_ALPHA1-3 : bond 0.06649 ( 15) link_ALPHA1-3 : angle 3.74459 ( 45) link_ALPHA1-6 : bond 0.04556 ( 9) link_ALPHA1-6 : angle 9.87587 ( 27) link_BETA1-3 : bond 0.08458 ( 3) link_BETA1-3 : angle 3.92413 ( 9) link_BETA1-4 : bond 0.06109 ( 51) link_BETA1-4 : angle 3.71473 ( 153) link_BETA2-3 : bond 0.01478 ( 3) link_BETA2-3 : angle 4.45172 ( 9) link_NAG-ASN : bond 0.03400 ( 51) link_NAG-ASN : angle 2.50053 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 585 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 GLN cc_start: 0.7794 (mt0) cc_final: 0.7536 (mt0) REVERT: A 849 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8773 (tp) REVERT: B 427 GLN cc_start: 0.7623 (mt0) cc_final: 0.7318 (mt0) REVERT: B 521 ASN cc_start: 0.8383 (m-40) cc_final: 0.8058 (m110) REVERT: B 766 HIS cc_start: 0.7671 (m90) cc_final: 0.7467 (m170) REVERT: B 994 GLN cc_start: 0.7395 (mt0) cc_final: 0.7190 (mt0) REVERT: C 505 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7811 (mtm180) REVERT: C 539 ASP cc_start: 0.8329 (m-30) cc_final: 0.7954 (m-30) REVERT: C 576 GLN cc_start: 0.7648 (mt0) cc_final: 0.7434 (mp10) REVERT: C 849 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8674 (tp) outliers start: 27 outliers final: 4 residues processed: 600 average time/residue: 0.6531 time to fit residues: 458.8120 Evaluate side-chains 341 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 335 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1097 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 812 ASN A 815 GLN A 819 GLN A1063 GLN A1163 ASN A1208 GLN B 261 GLN B 280 GLN B 521 ASN B 708 GLN B 812 ASN B 833 GLN B 974 GLN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN B1208 GLN C 280 GLN C 436 ASN C 466 GLN C 766 HIS C 812 ASN C 815 GLN C 833 GLN C1056 GLN C1063 GLN C1208 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.149608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.124051 restraints weight = 31169.437| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.65 r_work: 0.3050 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29610 Z= 0.197 Angle : 0.787 10.344 40563 Z= 0.386 Chirality : 0.049 0.241 4893 Planarity : 0.004 0.036 4974 Dihedral : 13.407 114.768 6689 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.52 % Allowed : 8.33 % Favored : 89.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3447 helix: 0.96 (0.20), residues: 687 sheet: 0.49 (0.16), residues: 834 loop : 0.31 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 841 TYR 0.024 0.002 TYR A 909 PHE 0.025 0.002 PHE A 850 TRP 0.012 0.002 TRP B 960 HIS 0.005 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00434 (29421) covalent geometry : angle 0.72698 (40047) SS BOND : bond 0.00487 ( 51) SS BOND : angle 1.41522 ( 102) hydrogen bonds : bond 0.05401 ( 1157) hydrogen bonds : angle 6.21420 ( 3024) link_ALPHA1-2 : bond 0.00462 ( 6) link_ALPHA1-2 : angle 1.77560 ( 18) link_ALPHA1-3 : bond 0.00744 ( 15) link_ALPHA1-3 : angle 2.37650 ( 45) link_ALPHA1-6 : bond 0.00527 ( 9) link_ALPHA1-6 : angle 1.98530 ( 27) link_BETA1-3 : bond 0.01285 ( 3) link_BETA1-3 : angle 2.77060 ( 9) link_BETA1-4 : bond 0.01019 ( 51) link_BETA1-4 : angle 3.21849 ( 153) link_BETA2-3 : bond 0.00490 ( 3) link_BETA2-3 : angle 0.97239 ( 9) link_NAG-ASN : bond 0.00649 ( 51) link_NAG-ASN : angle 3.27844 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 412 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7641 (tt0) cc_final: 0.7383 (tt0) REVERT: A 272 ASP cc_start: 0.8535 (t0) cc_final: 0.8302 (t0) REVERT: A 652 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7195 (mtt-85) REVERT: A 728 LYS cc_start: 0.8341 (mttt) cc_final: 0.7894 (mmtm) REVERT: A 907 GLN cc_start: 0.8435 (pt0) cc_final: 0.8228 (pt0) REVERT: A 1039 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: A 1112 LYS cc_start: 0.8315 (mttp) cc_final: 0.7830 (mppt) REVERT: B 160 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7551 (mtmt) REVERT: B 207 TYR cc_start: 0.8619 (p90) cc_final: 0.8326 (p90) REVERT: B 413 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8121 (mttm) REVERT: B 427 GLN cc_start: 0.8584 (mt0) cc_final: 0.8292 (mt0) REVERT: B 536 GLU cc_start: 0.8330 (pt0) cc_final: 0.8083 (pt0) REVERT: B 728 LYS cc_start: 0.8248 (mttt) cc_final: 0.7786 (mmtm) REVERT: B 849 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8778 (tt) REVERT: B 900 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8559 (mm) REVERT: B 1112 LYS cc_start: 0.8003 (mttp) cc_final: 0.7718 (mptt) REVERT: C 191 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7955 (m) REVERT: C 536 GLU cc_start: 0.8424 (pt0) cc_final: 0.8028 (pt0) REVERT: C 576 GLN cc_start: 0.8433 (mt0) cc_final: 0.7996 (mp10) REVERT: C 618 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: C 728 LYS cc_start: 0.8210 (mttt) cc_final: 0.7794 (mmtm) REVERT: C 907 GLN cc_start: 0.8520 (pt0) cc_final: 0.8267 (pt0) REVERT: C 992 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 995 LYS cc_start: 0.7885 (mppt) cc_final: 0.7602 (mptp) REVERT: C 1039 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: C 1056 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7992 (tt0) outliers start: 75 outliers final: 18 residues processed: 462 average time/residue: 0.6220 time to fit residues: 339.4428 Evaluate side-chains 337 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 1039 GLU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 1008 MET Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 145 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 67 optimal weight: 0.0060 chunk 328 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 82 optimal weight: 0.0050 chunk 15 optimal weight: 0.2980 chunk 129 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A 819 GLN A 833 GLN A 927 GLN B 576 GLN B 599 GLN B 708 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN B 974 GLN B1097 GLN B1169 ASN C 261 GLN C 408 ASN C 708 GLN C 766 HIS C 812 ASN C 833 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.124560 restraints weight = 31240.221| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.77 r_work: 0.3067 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29610 Z= 0.135 Angle : 0.656 9.183 40563 Z= 0.317 Chirality : 0.045 0.187 4893 Planarity : 0.004 0.039 4974 Dihedral : 10.969 96.312 6679 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 9.58 % Favored : 87.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3447 helix: 0.95 (0.20), residues: 720 sheet: 0.30 (0.16), residues: 846 loop : 0.22 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.019 0.001 TYR B 909 PHE 0.023 0.001 PHE B 850 TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00283 (29421) covalent geometry : angle 0.60775 (40047) SS BOND : bond 0.00503 ( 51) SS BOND : angle 1.30578 ( 102) hydrogen bonds : bond 0.04433 ( 1157) hydrogen bonds : angle 5.79234 ( 3024) link_ALPHA1-2 : bond 0.00436 ( 6) link_ALPHA1-2 : angle 1.69125 ( 18) link_ALPHA1-3 : bond 0.01020 ( 15) link_ALPHA1-3 : angle 1.54437 ( 45) link_ALPHA1-6 : bond 0.00721 ( 9) link_ALPHA1-6 : angle 1.82307 ( 27) link_BETA1-3 : bond 0.01351 ( 3) link_BETA1-3 : angle 2.27457 ( 9) link_BETA1-4 : bond 0.01058 ( 51) link_BETA1-4 : angle 2.74276 ( 153) link_BETA2-3 : bond 0.00564 ( 3) link_BETA2-3 : angle 1.81749 ( 9) link_NAG-ASN : bond 0.00612 ( 51) link_NAG-ASN : angle 2.56000 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 357 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.7788 (m-80) cc_final: 0.7506 (m-80) REVERT: A 565 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: A 652 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7791 (mtt-85) REVERT: A 728 LYS cc_start: 0.8330 (mttt) cc_final: 0.7922 (mmtm) REVERT: A 738 LEU cc_start: 0.8356 (tp) cc_final: 0.8108 (mm) REVERT: A 892 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: A 897 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7344 (mtpm) REVERT: A 907 GLN cc_start: 0.8271 (pt0) cc_final: 0.8055 (pt0) REVERT: A 1039 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: A 1069 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8117 (ttp80) REVERT: A 1112 LYS cc_start: 0.8311 (mttp) cc_final: 0.7864 (mppt) REVERT: B 413 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8249 (mttm) REVERT: B 427 GLN cc_start: 0.8628 (mt0) cc_final: 0.8350 (mt0) REVERT: B 618 GLN cc_start: 0.8146 (mt0) cc_final: 0.7891 (mm-40) REVERT: B 728 LYS cc_start: 0.8163 (mttt) cc_final: 0.7739 (mmtm) REVERT: B 849 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8823 (tt) REVERT: B 1105 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: B 1112 LYS cc_start: 0.8130 (mttp) cc_final: 0.7683 (mppt) REVERT: C 191 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.8009 (m) REVERT: C 576 GLN cc_start: 0.8351 (mt0) cc_final: 0.7885 (mp10) REVERT: C 618 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: C 652 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7693 (mmt-90) REVERT: C 728 LYS cc_start: 0.8242 (mttt) cc_final: 0.7806 (mmtm) REVERT: C 738 LEU cc_start: 0.8297 (tp) cc_final: 0.7937 (mm) REVERT: C 848 ASN cc_start: 0.8422 (t0) cc_final: 0.8199 (t0) REVERT: C 892 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: C 907 GLN cc_start: 0.8244 (pt0) cc_final: 0.8024 (pt0) REVERT: C 943 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: C 988 GLN cc_start: 0.7892 (tt0) cc_final: 0.7359 (mp10) REVERT: C 995 LYS cc_start: 0.7807 (mppt) cc_final: 0.7582 (mptp) REVERT: C 1039 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: C 1062 GLU cc_start: 0.7566 (tp30) cc_final: 0.7303 (tp30) outliers start: 94 outliers final: 32 residues processed: 421 average time/residue: 0.5763 time to fit residues: 290.1331 Evaluate side-chains 347 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1039 GLU Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 311 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 342 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 341 optimal weight: 0.6980 chunk 300 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN A 708 GLN A 812 ASN A 819 GLN A 927 GLN B 466 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 708 GLN C 812 ASN C 927 GLN C1145 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.121156 restraints weight = 30957.974| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.64 r_work: 0.3012 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29610 Z= 0.165 Angle : 0.666 10.381 40563 Z= 0.324 Chirality : 0.046 0.285 4893 Planarity : 0.004 0.042 4974 Dihedral : 9.204 86.768 6679 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.26 % Allowed : 10.62 % Favored : 86.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3447 helix: 1.20 (0.20), residues: 708 sheet: 0.27 (0.16), residues: 864 loop : 0.03 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 542 TYR 0.017 0.002 TYR B 909 PHE 0.021 0.002 PHE B 473 TRP 0.008 0.001 TRP B 310 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00368 (29421) covalent geometry : angle 0.62177 (40047) SS BOND : bond 0.00936 ( 51) SS BOND : angle 1.57404 ( 102) hydrogen bonds : bond 0.04542 ( 1157) hydrogen bonds : angle 5.63930 ( 3024) link_ALPHA1-2 : bond 0.00359 ( 6) link_ALPHA1-2 : angle 1.66307 ( 18) link_ALPHA1-3 : bond 0.00968 ( 15) link_ALPHA1-3 : angle 1.80509 ( 45) link_ALPHA1-6 : bond 0.00920 ( 9) link_ALPHA1-6 : angle 1.59604 ( 27) link_BETA1-3 : bond 0.01151 ( 3) link_BETA1-3 : angle 2.13575 ( 9) link_BETA1-4 : bond 0.00882 ( 51) link_BETA1-4 : angle 2.52957 ( 153) link_BETA2-3 : bond 0.00412 ( 3) link_BETA2-3 : angle 1.21415 ( 9) link_NAG-ASN : bond 0.00696 ( 51) link_NAG-ASN : angle 2.50997 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 338 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7597 (mttt) REVERT: A 193 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: A 272 ASP cc_start: 0.8565 (t0) cc_final: 0.8263 (t0) REVERT: A 536 GLU cc_start: 0.8481 (pt0) cc_final: 0.8058 (pm20) REVERT: A 542 ARG cc_start: 0.8778 (ptp90) cc_final: 0.8503 (mtt-85) REVERT: A 652 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7730 (mmt-90) REVERT: A 728 LYS cc_start: 0.8213 (mttt) cc_final: 0.7728 (mmtm) REVERT: A 849 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8922 (tp) REVERT: A 892 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: A 907 GLN cc_start: 0.8236 (pt0) cc_final: 0.8033 (pt0) REVERT: A 1019 PHE cc_start: 0.8325 (t80) cc_final: 0.8072 (t80) REVERT: A 1069 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: A 1112 LYS cc_start: 0.8370 (mttp) cc_final: 0.7841 (mppt) REVERT: B 36 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: B 161 MET cc_start: 0.8073 (mtp) cc_final: 0.7387 (mmt) REVERT: B 413 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8311 (mttm) REVERT: B 427 GLN cc_start: 0.8775 (mt0) cc_final: 0.8483 (mt0) REVERT: B 618 GLN cc_start: 0.8176 (mt0) cc_final: 0.7840 (mm-40) REVERT: B 728 LYS cc_start: 0.8226 (mttt) cc_final: 0.7756 (mmtm) REVERT: B 841 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7407 (tpt90) REVERT: B 849 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8851 (tt) REVERT: B 892 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: B 1105 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: B 1112 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: C 230 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: C 240 MET cc_start: 0.9172 (ttm) cc_final: 0.8823 (ttt) REVERT: C 261 GLN cc_start: 0.8700 (mt0) cc_final: 0.8482 (mt0) REVERT: C 576 GLN cc_start: 0.8399 (mt0) cc_final: 0.7911 (mp10) REVERT: C 618 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: C 708 GLN cc_start: 0.8601 (tp40) cc_final: 0.8390 (tp-100) REVERT: C 728 LYS cc_start: 0.8213 (mttt) cc_final: 0.7774 (mmtm) REVERT: C 848 ASN cc_start: 0.8487 (t0) cc_final: 0.8270 (t0) REVERT: C 849 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8863 (tp) REVERT: C 892 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: C 907 GLN cc_start: 0.8275 (pt0) cc_final: 0.8063 (pt0) REVERT: C 943 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: C 1039 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: C 1214 ILE cc_start: 0.8588 (pt) cc_final: 0.8318 (pt) outliers start: 97 outliers final: 42 residues processed: 412 average time/residue: 0.5594 time to fit residues: 275.7830 Evaluate side-chains 373 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 186 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 466 GLN A 812 ASN A 819 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN A1169 ASN B 348 HIS B 708 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN B1132 ASN C 348 HIS C 765 ASN C 812 ASN C 819 GLN C1056 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117968 restraints weight = 30799.625| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.63 r_work: 0.2980 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29610 Z= 0.218 Angle : 0.702 8.743 40563 Z= 0.344 Chirality : 0.047 0.243 4893 Planarity : 0.004 0.047 4974 Dihedral : 8.980 89.195 6678 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.40 % Allowed : 10.69 % Favored : 84.91 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3447 helix: 1.05 (0.19), residues: 738 sheet: 0.12 (0.17), residues: 873 loop : -0.18 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 652 TYR 0.019 0.002 TYR B 909 PHE 0.024 0.002 PHE A 786 TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00505 (29421) covalent geometry : angle 0.66102 (40047) SS BOND : bond 0.00608 ( 51) SS BOND : angle 1.69211 ( 102) hydrogen bonds : bond 0.04919 ( 1157) hydrogen bonds : angle 5.67530 ( 3024) link_ALPHA1-2 : bond 0.00374 ( 6) link_ALPHA1-2 : angle 1.61647 ( 18) link_ALPHA1-3 : bond 0.00939 ( 15) link_ALPHA1-3 : angle 1.63487 ( 45) link_ALPHA1-6 : bond 0.00850 ( 9) link_ALPHA1-6 : angle 1.57859 ( 27) link_BETA1-3 : bond 0.01073 ( 3) link_BETA1-3 : angle 2.12786 ( 9) link_BETA1-4 : bond 0.00784 ( 51) link_BETA1-4 : angle 2.42735 ( 153) link_BETA2-3 : bond 0.00405 ( 3) link_BETA2-3 : angle 1.33304 ( 9) link_NAG-ASN : bond 0.00527 ( 51) link_NAG-ASN : angle 2.57718 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 314 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7686 (mttt) REVERT: A 36 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: A 108 ASP cc_start: 0.7451 (t0) cc_final: 0.7122 (t70) REVERT: A 193 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: A 542 ARG cc_start: 0.8804 (ptp90) cc_final: 0.8466 (mtt-85) REVERT: A 652 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7859 (mmt-90) REVERT: A 728 LYS cc_start: 0.8261 (mttt) cc_final: 0.7760 (mmtm) REVERT: A 849 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 892 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: A 907 GLN cc_start: 0.8344 (pt0) cc_final: 0.8123 (pt0) REVERT: A 1069 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8092 (ttp80) REVERT: A 1112 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7905 (mppt) REVERT: B 27 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7565 (mttt) REVERT: B 60 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: B 161 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7509 (mmt) REVERT: B 193 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7658 (m-40) REVERT: B 207 TYR cc_start: 0.8727 (p90) cc_final: 0.8435 (p90) REVERT: B 427 GLN cc_start: 0.8909 (mt0) cc_final: 0.8659 (mt0) REVERT: B 450 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 722 LEU cc_start: 0.7300 (tt) cc_final: 0.6775 (mt) REVERT: B 728 LYS cc_start: 0.8263 (mttt) cc_final: 0.7747 (mmtm) REVERT: B 841 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7593 (tpt170) REVERT: B 849 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 892 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 960 TRP cc_start: 0.6673 (OUTLIER) cc_final: 0.6280 (t60) REVERT: B 1003 GLN cc_start: 0.8207 (mt0) cc_final: 0.7881 (tt0) REVERT: B 1105 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: B 1112 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7972 (mptt) REVERT: B 1169 ASN cc_start: 0.7859 (t0) cc_final: 0.7528 (m-40) REVERT: C 60 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: C 240 MET cc_start: 0.9159 (ttm) cc_final: 0.8831 (ttt) REVERT: C 261 GLN cc_start: 0.8757 (mt0) cc_final: 0.8548 (mt0) REVERT: C 652 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: C 708 GLN cc_start: 0.8656 (tp40) cc_final: 0.8415 (tp-100) REVERT: C 728 LYS cc_start: 0.8254 (mttt) cc_final: 0.7780 (mmtm) REVERT: C 849 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8894 (tp) REVERT: C 892 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: C 907 GLN cc_start: 0.8451 (pt0) cc_final: 0.8241 (pt0) REVERT: C 943 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: C 1039 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: C 1056 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8317 (tt0) outliers start: 131 outliers final: 50 residues processed: 413 average time/residue: 0.5398 time to fit residues: 268.7476 Evaluate side-chains 367 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 992 GLU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 294 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 312 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 812 ASN A 819 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1119 GLN B 812 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN C 111 GLN C 765 ASN C 812 ASN C 993 ASN C1063 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.119380 restraints weight = 30789.163| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.66 r_work: 0.2993 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29610 Z= 0.155 Angle : 0.646 8.283 40563 Z= 0.314 Chirality : 0.045 0.223 4893 Planarity : 0.004 0.045 4974 Dihedral : 8.574 87.598 6678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.53 % Allowed : 11.66 % Favored : 84.81 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3447 helix: 1.06 (0.19), residues: 744 sheet: 0.15 (0.16), residues: 888 loop : -0.17 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.018 0.001 TYR C 207 PHE 0.026 0.001 PHE A 786 TRP 0.008 0.001 TRP B 310 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00345 (29421) covalent geometry : angle 0.60655 (40047) SS BOND : bond 0.00459 ( 51) SS BOND : angle 1.40119 ( 102) hydrogen bonds : bond 0.04422 ( 1157) hydrogen bonds : angle 5.55411 ( 3024) link_ALPHA1-2 : bond 0.00363 ( 6) link_ALPHA1-2 : angle 1.59482 ( 18) link_ALPHA1-3 : bond 0.00922 ( 15) link_ALPHA1-3 : angle 1.62214 ( 45) link_ALPHA1-6 : bond 0.00870 ( 9) link_ALPHA1-6 : angle 1.53658 ( 27) link_BETA1-3 : bond 0.01069 ( 3) link_BETA1-3 : angle 1.95152 ( 9) link_BETA1-4 : bond 0.00763 ( 51) link_BETA1-4 : angle 2.40150 ( 153) link_BETA2-3 : bond 0.00403 ( 3) link_BETA2-3 : angle 1.30753 ( 9) link_NAG-ASN : bond 0.00675 ( 51) link_NAG-ASN : angle 2.35527 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 309 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: A 108 ASP cc_start: 0.7459 (t0) cc_final: 0.7167 (t70) REVERT: A 536 GLU cc_start: 0.8449 (pt0) cc_final: 0.7993 (pm20) REVERT: A 542 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8399 (mtt-85) REVERT: A 652 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7809 (mmt-90) REVERT: A 728 LYS cc_start: 0.8276 (mttt) cc_final: 0.7774 (mmtm) REVERT: A 849 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8926 (tp) REVERT: A 892 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: A 907 GLN cc_start: 0.8364 (pt0) cc_final: 0.8132 (pt0) REVERT: A 1019 PHE cc_start: 0.8437 (t80) cc_final: 0.8155 (t80) REVERT: A 1069 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8103 (ttp80) REVERT: A 1112 LYS cc_start: 0.8269 (mttp) cc_final: 0.7849 (mppt) REVERT: B 27 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7539 (mttt) REVERT: B 161 MET cc_start: 0.8239 (mtp) cc_final: 0.7542 (mmt) REVERT: B 193 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7580 (m-40) REVERT: B 207 TYR cc_start: 0.8648 (p90) cc_final: 0.8156 (p90) REVERT: B 427 GLN cc_start: 0.8911 (mt0) cc_final: 0.8616 (mt0) REVERT: B 450 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8314 (mm) REVERT: B 473 PHE cc_start: 0.7880 (m-80) cc_final: 0.7585 (p90) REVERT: B 728 LYS cc_start: 0.8257 (mttt) cc_final: 0.7743 (mmtm) REVERT: B 841 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7588 (tpt170) REVERT: B 849 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8904 (tt) REVERT: B 892 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: B 960 TRP cc_start: 0.6669 (OUTLIER) cc_final: 0.6399 (t60) REVERT: B 1003 GLN cc_start: 0.8202 (mt0) cc_final: 0.7891 (tt0) REVERT: B 1105 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: B 1112 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7843 (mptt) REVERT: B 1169 ASN cc_start: 0.7845 (t0) cc_final: 0.7482 (m-40) REVERT: C 36 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: C 60 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: C 179 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9089 (pt) REVERT: C 240 MET cc_start: 0.9160 (ttm) cc_final: 0.8823 (ttt) REVERT: C 261 GLN cc_start: 0.8694 (mt0) cc_final: 0.8485 (mt0) REVERT: C 618 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: C 652 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7817 (mtt-85) REVERT: C 708 GLN cc_start: 0.8628 (tp40) cc_final: 0.8391 (tp-100) REVERT: C 728 LYS cc_start: 0.8242 (mttt) cc_final: 0.7765 (mmtm) REVERT: C 849 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8930 (tp) REVERT: C 943 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: C 1039 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8022 (mm-30) outliers start: 105 outliers final: 48 residues processed: 385 average time/residue: 0.5401 time to fit residues: 251.2287 Evaluate side-chains 367 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 618 GLN Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 155 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 303 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 812 ASN A 819 GLN A 993 ASN A1119 GLN B 708 GLN B 812 ASN B 927 GLN B1097 GLN C 765 ASN C 812 ASN C1042 ASN C1056 GLN C1169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.142379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116366 restraints weight = 31024.086| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.70 r_work: 0.2942 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 29610 Z= 0.248 Angle : 0.726 9.161 40563 Z= 0.356 Chirality : 0.048 0.282 4893 Planarity : 0.005 0.050 4974 Dihedral : 8.833 89.558 6678 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.97 % Allowed : 11.79 % Favored : 84.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3447 helix: 1.02 (0.19), residues: 738 sheet: 0.06 (0.17), residues: 840 loop : -0.36 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 62 TYR 0.015 0.002 TYR C 184 PHE 0.030 0.002 PHE A 786 TRP 0.007 0.001 TRP B 310 HIS 0.008 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00580 (29421) covalent geometry : angle 0.68632 (40047) SS BOND : bond 0.00643 ( 51) SS BOND : angle 1.88017 ( 102) hydrogen bonds : bond 0.05118 ( 1157) hydrogen bonds : angle 5.71077 ( 3024) link_ALPHA1-2 : bond 0.00276 ( 6) link_ALPHA1-2 : angle 1.68030 ( 18) link_ALPHA1-3 : bond 0.00841 ( 15) link_ALPHA1-3 : angle 1.58112 ( 45) link_ALPHA1-6 : bond 0.00857 ( 9) link_ALPHA1-6 : angle 1.55514 ( 27) link_BETA1-3 : bond 0.00970 ( 3) link_BETA1-3 : angle 2.19477 ( 9) link_BETA1-4 : bond 0.00732 ( 51) link_BETA1-4 : angle 2.35214 ( 153) link_BETA2-3 : bond 0.00225 ( 3) link_BETA2-3 : angle 1.09759 ( 9) link_NAG-ASN : bond 0.00570 ( 51) link_NAG-ASN : angle 2.60758 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 300 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6508 (mp10) REVERT: A 108 ASP cc_start: 0.7637 (t0) cc_final: 0.7345 (t70) REVERT: A 193 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: A 413 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8396 (mttm) REVERT: A 542 ARG cc_start: 0.8753 (ptp90) cc_final: 0.8395 (mtt-85) REVERT: A 614 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8268 (mtt-85) REVERT: A 652 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7880 (mmt-90) REVERT: A 728 LYS cc_start: 0.8253 (mttt) cc_final: 0.7712 (mmtm) REVERT: A 849 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8727 (tt) REVERT: A 892 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: A 907 GLN cc_start: 0.8378 (pt0) cc_final: 0.8151 (pt0) REVERT: A 1069 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8040 (ttp80) REVERT: A 1112 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7846 (mptt) REVERT: B 27 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7652 (mttt) REVERT: B 60 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: B 161 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7513 (mmt) REVERT: B 193 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: B 427 GLN cc_start: 0.8897 (mt0) cc_final: 0.8610 (mt0) REVERT: B 450 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 722 LEU cc_start: 0.7401 (tt) cc_final: 0.6876 (mt) REVERT: B 728 LYS cc_start: 0.8276 (mttt) cc_final: 0.7714 (mmtm) REVERT: B 757 MET cc_start: 0.8176 (mtt) cc_final: 0.7838 (mtt) REVERT: B 849 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 892 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: B 960 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.6345 (t60) REVERT: B 1084 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8322 (mm-40) REVERT: B 1105 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: B 1112 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7842 (mptt) REVERT: C 60 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: C 240 MET cc_start: 0.9148 (ttm) cc_final: 0.8813 (ttt) REVERT: C 533 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 652 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7672 (mtt-85) REVERT: C 728 LYS cc_start: 0.8266 (mttt) cc_final: 0.7761 (mmtm) REVERT: C 849 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8910 (tp) REVERT: C 892 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: C 943 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8265 (tpp) REVERT: C 1039 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: C 1056 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8323 (tt0) outliers start: 118 outliers final: 59 residues processed: 392 average time/residue: 0.5387 time to fit residues: 255.1101 Evaluate side-chains 372 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 286 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 618 GLN Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 309 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 341 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 812 ASN A 819 GLN A 993 ASN A1119 GLN A1132 ASN B 812 ASN B 819 GLN C 599 GLN C 708 GLN C 765 ASN C 812 ASN C1132 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117246 restraints weight = 31058.123| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.72 r_work: 0.2961 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29610 Z= 0.198 Angle : 0.686 10.404 40563 Z= 0.335 Chirality : 0.046 0.250 4893 Planarity : 0.004 0.045 4974 Dihedral : 8.642 88.676 6678 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.70 % Allowed : 12.47 % Favored : 83.84 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3447 helix: 0.96 (0.19), residues: 744 sheet: 0.02 (0.17), residues: 840 loop : -0.40 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 269 TYR 0.013 0.002 TYR B 909 PHE 0.030 0.002 PHE A 786 TRP 0.008 0.001 TRP B 310 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00454 (29421) covalent geometry : angle 0.64547 (40047) SS BOND : bond 0.00558 ( 51) SS BOND : angle 1.80381 ( 102) hydrogen bonds : bond 0.04765 ( 1157) hydrogen bonds : angle 5.64364 ( 3024) link_ALPHA1-2 : bond 0.00281 ( 6) link_ALPHA1-2 : angle 1.64932 ( 18) link_ALPHA1-3 : bond 0.00847 ( 15) link_ALPHA1-3 : angle 1.54118 ( 45) link_ALPHA1-6 : bond 0.00848 ( 9) link_ALPHA1-6 : angle 1.48517 ( 27) link_BETA1-3 : bond 0.00965 ( 3) link_BETA1-3 : angle 2.05634 ( 9) link_BETA1-4 : bond 0.00710 ( 51) link_BETA1-4 : angle 2.28193 ( 153) link_BETA2-3 : bond 0.00287 ( 3) link_BETA2-3 : angle 1.19602 ( 9) link_NAG-ASN : bond 0.00502 ( 51) link_NAG-ASN : angle 2.56189 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 288 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: A 108 ASP cc_start: 0.7601 (t0) cc_final: 0.7244 (t70) REVERT: A 193 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: A 413 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (mttm) REVERT: A 542 ARG cc_start: 0.8730 (ptp90) cc_final: 0.8402 (mtt-85) REVERT: A 652 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7880 (mmt-90) REVERT: A 728 LYS cc_start: 0.8311 (mttt) cc_final: 0.7760 (mmtm) REVERT: A 849 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8918 (tp) REVERT: A 892 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: A 907 GLN cc_start: 0.8345 (pt0) cc_final: 0.8129 (pt0) REVERT: A 1069 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8064 (ttp80) REVERT: A 1112 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7845 (mptt) REVERT: B 60 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6468 (mp10) REVERT: B 161 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: B 193 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7589 (m-40) REVERT: B 218 ASN cc_start: 0.7983 (p0) cc_final: 0.7732 (p0) REVERT: B 427 GLN cc_start: 0.8899 (mt0) cc_final: 0.8613 (mt0) REVERT: B 450 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8343 (mm) REVERT: B 473 PHE cc_start: 0.7885 (m-80) cc_final: 0.7586 (p90) REVERT: B 722 LEU cc_start: 0.7337 (tt) cc_final: 0.6820 (mt) REVERT: B 728 LYS cc_start: 0.8259 (mttt) cc_final: 0.7690 (mmtm) REVERT: B 757 MET cc_start: 0.8224 (mtt) cc_final: 0.7978 (mtt) REVERT: B 841 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7609 (tpt170) REVERT: B 849 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8893 (tt) REVERT: B 892 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: B 960 TRP cc_start: 0.6659 (OUTLIER) cc_final: 0.6352 (t60) REVERT: B 1003 GLN cc_start: 0.8269 (mt0) cc_final: 0.7860 (tt0) REVERT: B 1084 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8319 (mm-40) REVERT: B 1105 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: B 1112 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7853 (mptt) REVERT: C 60 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: C 240 MET cc_start: 0.9160 (ttm) cc_final: 0.8806 (ttt) REVERT: C 261 GLN cc_start: 0.8760 (mt0) cc_final: 0.8544 (mt0) REVERT: C 533 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8165 (p) REVERT: C 649 TYR cc_start: 0.8627 (m-80) cc_final: 0.8390 (m-80) REVERT: C 652 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: C 728 LYS cc_start: 0.8271 (mttt) cc_final: 0.7757 (mmtm) REVERT: C 849 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8919 (tp) REVERT: C 892 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: C 943 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: C 1039 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7972 (mm-30) outliers start: 110 outliers final: 60 residues processed: 376 average time/residue: 0.5483 time to fit residues: 248.6286 Evaluate side-chains 371 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 618 GLN Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 113 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 166 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 287 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A 819 GLN A 993 ASN A1132 ASN B 812 ASN C 637 ASN C 708 GLN C 765 ASN C 812 ASN C1132 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.145138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119290 restraints weight = 30905.574| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.71 r_work: 0.2975 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29610 Z= 0.148 Angle : 0.641 10.907 40563 Z= 0.311 Chirality : 0.044 0.243 4893 Planarity : 0.004 0.044 4974 Dihedral : 8.282 86.647 6678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.02 % Allowed : 13.07 % Favored : 83.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3447 helix: 1.11 (0.19), residues: 744 sheet: 0.08 (0.17), residues: 843 loop : -0.38 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.014 0.001 TYR B 909 PHE 0.031 0.001 PHE A 786 TRP 0.009 0.001 TRP B 310 HIS 0.003 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00328 (29421) covalent geometry : angle 0.60015 (40047) SS BOND : bond 0.00634 ( 51) SS BOND : angle 1.62165 ( 102) hydrogen bonds : bond 0.04316 ( 1157) hydrogen bonds : angle 5.52247 ( 3024) link_ALPHA1-2 : bond 0.00293 ( 6) link_ALPHA1-2 : angle 1.62581 ( 18) link_ALPHA1-3 : bond 0.00824 ( 15) link_ALPHA1-3 : angle 1.50986 ( 45) link_ALPHA1-6 : bond 0.00846 ( 9) link_ALPHA1-6 : angle 1.46075 ( 27) link_BETA1-3 : bond 0.00950 ( 3) link_BETA1-3 : angle 1.89678 ( 9) link_BETA1-4 : bond 0.00712 ( 51) link_BETA1-4 : angle 2.20231 ( 153) link_BETA2-3 : bond 0.00429 ( 3) link_BETA2-3 : angle 1.23088 ( 9) link_NAG-ASN : bond 0.00485 ( 51) link_NAG-ASN : angle 2.51105 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 308 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6430 (mp10) REVERT: A 108 ASP cc_start: 0.7555 (t0) cc_final: 0.7192 (t70) REVERT: A 272 ASP cc_start: 0.8578 (t0) cc_final: 0.8213 (t0) REVERT: A 413 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8424 (mttm) REVERT: A 450 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 542 ARG cc_start: 0.8743 (ptp90) cc_final: 0.8426 (mtt-85) REVERT: A 652 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7853 (mmt-90) REVERT: A 728 LYS cc_start: 0.8295 (mttt) cc_final: 0.7760 (mmtm) REVERT: A 849 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 892 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: A 907 GLN cc_start: 0.8407 (pt0) cc_final: 0.8187 (pt0) REVERT: A 1019 PHE cc_start: 0.8406 (t80) cc_final: 0.8153 (t80) REVERT: A 1069 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8029 (ttp80) REVERT: A 1112 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7863 (mptt) REVERT: B 161 MET cc_start: 0.8061 (mtp) cc_final: 0.7386 (mmt) REVERT: B 193 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7604 (m-40) REVERT: B 207 TYR cc_start: 0.8623 (p90) cc_final: 0.8136 (p90) REVERT: B 427 GLN cc_start: 0.8882 (mt0) cc_final: 0.8598 (mt0) REVERT: B 450 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 473 PHE cc_start: 0.7857 (m-80) cc_final: 0.7606 (p90) REVERT: B 722 LEU cc_start: 0.7346 (tt) cc_final: 0.6810 (mt) REVERT: B 728 LYS cc_start: 0.8291 (mttt) cc_final: 0.7708 (mmtm) REVERT: B 841 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7592 (tpt170) REVERT: B 849 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8921 (tt) REVERT: B 892 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: B 960 TRP cc_start: 0.6712 (OUTLIER) cc_final: 0.6333 (t60) REVERT: B 1003 GLN cc_start: 0.8219 (mt0) cc_final: 0.7854 (tt0) REVERT: B 1105 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: B 1112 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (mptt) REVERT: C 240 MET cc_start: 0.9156 (ttm) cc_final: 0.8819 (ttt) REVERT: C 533 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8191 (p) REVERT: C 618 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: C 652 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (mtt-85) REVERT: C 728 LYS cc_start: 0.8276 (mttt) cc_final: 0.7754 (mmtm) REVERT: C 849 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8911 (tp) REVERT: C 892 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: C 1039 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7944 (mm-30) outliers start: 90 outliers final: 47 residues processed: 375 average time/residue: 0.5493 time to fit residues: 248.3155 Evaluate side-chains 362 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 618 GLN Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1039 GLU Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 105 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 148 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 265 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 86 optimal weight: 0.0070 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 812 ASN A 819 GLN A 993 ASN A1132 ASN B 812 ASN B 819 GLN B1063 GLN C 708 GLN C 765 ASN C 812 ASN C1132 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.146920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122309 restraints weight = 30865.091| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.71 r_work: 0.3016 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29610 Z= 0.121 Angle : 0.606 10.872 40563 Z= 0.292 Chirality : 0.043 0.239 4893 Planarity : 0.004 0.043 4974 Dihedral : 7.834 84.401 6678 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.22 % Allowed : 14.25 % Favored : 83.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3447 helix: 1.17 (0.19), residues: 762 sheet: 0.01 (0.17), residues: 870 loop : -0.29 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.015 0.001 TYR C 207 PHE 0.030 0.001 PHE A 786 TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00263 (29421) covalent geometry : angle 0.56586 (40047) SS BOND : bond 0.00480 ( 51) SS BOND : angle 1.48723 ( 102) hydrogen bonds : bond 0.03933 ( 1157) hydrogen bonds : angle 5.37354 ( 3024) link_ALPHA1-2 : bond 0.00312 ( 6) link_ALPHA1-2 : angle 1.60973 ( 18) link_ALPHA1-3 : bond 0.00778 ( 15) link_ALPHA1-3 : angle 1.50245 ( 45) link_ALPHA1-6 : bond 0.00835 ( 9) link_ALPHA1-6 : angle 1.48110 ( 27) link_BETA1-3 : bond 0.00905 ( 3) link_BETA1-3 : angle 1.75634 ( 9) link_BETA1-4 : bond 0.00744 ( 51) link_BETA1-4 : angle 2.14487 ( 153) link_BETA2-3 : bond 0.00442 ( 3) link_BETA2-3 : angle 1.17695 ( 9) link_NAG-ASN : bond 0.00491 ( 51) link_NAG-ASN : angle 2.39241 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.7492 (t0) cc_final: 0.7229 (t70) REVERT: A 272 ASP cc_start: 0.8529 (t0) cc_final: 0.8077 (t0) REVERT: A 413 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8334 (mttm) REVERT: A 450 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8364 (mm) REVERT: A 542 ARG cc_start: 0.8724 (ptp90) cc_final: 0.8426 (mtt-85) REVERT: A 652 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7806 (mmt-90) REVERT: A 728 LYS cc_start: 0.8401 (mttt) cc_final: 0.7880 (mmtm) REVERT: A 849 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 907 GLN cc_start: 0.8328 (pt0) cc_final: 0.8115 (pt0) REVERT: A 1019 PHE cc_start: 0.8264 (t80) cc_final: 0.8055 (t80) REVERT: A 1069 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7950 (ttp80) REVERT: A 1112 LYS cc_start: 0.8289 (mttp) cc_final: 0.7880 (mptt) REVERT: B 161 MET cc_start: 0.8094 (mtp) cc_final: 0.7359 (mmt) REVERT: B 193 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (m-40) REVERT: B 207 TYR cc_start: 0.8556 (p90) cc_final: 0.8052 (p90) REVERT: B 427 GLN cc_start: 0.8853 (mt0) cc_final: 0.8595 (mt0) REVERT: B 450 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8300 (mm) REVERT: B 722 LEU cc_start: 0.7295 (tt) cc_final: 0.6796 (mt) REVERT: B 728 LYS cc_start: 0.8324 (mttt) cc_final: 0.7775 (mmtm) REVERT: B 849 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8900 (tt) REVERT: B 944 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 960 TRP cc_start: 0.6645 (OUTLIER) cc_final: 0.6166 (t60) REVERT: B 1003 GLN cc_start: 0.8147 (mt0) cc_final: 0.7823 (tt0) REVERT: B 1039 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7535 (mm-30) REVERT: B 1105 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: B 1112 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7858 (mmtm) REVERT: C 240 MET cc_start: 0.9158 (ttm) cc_final: 0.8820 (ttt) REVERT: C 533 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 618 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: C 728 LYS cc_start: 0.8293 (mttt) cc_final: 0.7770 (mmtm) REVERT: C 849 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8948 (tp) outliers start: 66 outliers final: 35 residues processed: 370 average time/residue: 0.5560 time to fit residues: 247.1193 Evaluate side-chains 357 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 819 GLN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1069 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1095 SER Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 132 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 314 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 332 optimal weight: 0.5980 chunk 317 optimal weight: 0.0770 chunk 340 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN A 819 GLN A 993 ASN A1132 ASN A1212 GLN B 261 GLN B 812 ASN B 819 GLN B1212 GLN C 261 GLN C 708 GLN C 765 ASN C 812 ASN C1031 GLN C1042 ASN C1132 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121425 restraints weight = 31235.159| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.67 r_work: 0.3034 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29610 Z= 0.126 Angle : 0.614 10.739 40563 Z= 0.298 Chirality : 0.043 0.241 4893 Planarity : 0.004 0.043 4974 Dihedral : 7.740 84.635 6678 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.95 % Allowed : 14.52 % Favored : 83.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3447 helix: 1.17 (0.19), residues: 762 sheet: 0.01 (0.17), residues: 870 loop : -0.27 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1069 TYR 0.015 0.001 TYR C 207 PHE 0.032 0.001 PHE A 786 TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS A1146 Details of bonding type rmsd covalent geometry : bond 0.00277 (29421) covalent geometry : angle 0.57268 (40047) SS BOND : bond 0.00474 ( 51) SS BOND : angle 1.85023 ( 102) hydrogen bonds : bond 0.03966 ( 1157) hydrogen bonds : angle 5.35772 ( 3024) link_ALPHA1-2 : bond 0.00318 ( 6) link_ALPHA1-2 : angle 1.60125 ( 18) link_ALPHA1-3 : bond 0.00758 ( 15) link_ALPHA1-3 : angle 1.47444 ( 45) link_ALPHA1-6 : bond 0.00803 ( 9) link_ALPHA1-6 : angle 1.49589 ( 27) link_BETA1-3 : bond 0.00881 ( 3) link_BETA1-3 : angle 1.78045 ( 9) link_BETA1-4 : bond 0.00733 ( 51) link_BETA1-4 : angle 2.12916 ( 153) link_BETA2-3 : bond 0.00389 ( 3) link_BETA2-3 : angle 1.09010 ( 9) link_NAG-ASN : bond 0.00482 ( 51) link_NAG-ASN : angle 2.38214 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10127.22 seconds wall clock time: 173 minutes 27.00 seconds (10407.00 seconds total)