Starting phenix.real_space_refine on Fri Mar 6 07:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.map" model { file = "/net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q06_20544/03_2026/6q06_20544.cif" } resolution = 2.7 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= 0.103 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 18126 2.51 5 N 4533 2.21 5 O 6120 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: 28926 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 6.89, per 1000 atoms: 0.24 Number of scatterers: 28926 At special positions: 0 Unit cell: (142.8, 153.3, 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 6120 8.00 N 4533 7.00 C 18126 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=2.02 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=2.10 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 " BETA1-4 " 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 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 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 " BETA2-3 " GAL N 1 " - " SIA N 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL Y 1 " - " SIA Y 2 " " GAL j 1 " - " SIA j 2 " 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: 3.06 Conformation dependent library (CDL) restraints added in 931.6 milliseconds 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: 1.52 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: 3.773A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.028A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.319A 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: 3.825A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 5.380A 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: 3.917A 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: 3.838A 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: 3.679A 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: 4.085A 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: 3.854A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 4.028A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.838A 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: 3.679A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.599A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.039A 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: 7.166A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.933A 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: 6.235A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.527A 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: 5.470A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 5.656A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.741A 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: 3.836A 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: 5.927A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.837A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.244A 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: 7.166A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.418A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.863A 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: 6.615A 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: 5.361A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.731A 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: 6.527A 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: 5.655A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.741A 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: 3.836A pdb=" N LYS B 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.927A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE7, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.039A 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: 7.166A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.292A 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: 6.418A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.005A 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: 5.425A 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: 4.863A 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: 3.523A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.235A 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: 5.927A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 3.62 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: 4509 1.26 - 1.46: 12114 1.46 - 1.66: 12507 1.66 - 1.85: 216 Bond restraints: 29349 Sorted by residual: bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.09e+02 bond pdb=" C CYS C 383 " pdb=" O CYS C 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 A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.06e+02 bond pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 bond pdb=" N CYS A 383 " pdb=" CA CYS A 383 " ideal model delta sigma weight residual 1.455 1.665 -0.210 1.33e-02 5.65e+03 2.49e+02 ... (remaining 29344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 38453 4.37 - 8.74: 1342 8.74 - 13.11: 99 13.11 - 17.48: 21 17.48 - 21.85: 33 Bond angle restraints: 39948 Sorted by residual: angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 120.92 142.21 -21.29 1.15e+00 7.56e-01 3.43e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.17 -21.25 1.15e+00 7.56e-01 3.42e+02 angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.13 -21.21 1.15e+00 7.56e-01 3.40e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 115.86 94.46 21.40 1.24e+00 6.50e-01 2.98e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 115.86 94.47 21.39 1.24e+00 6.50e-01 2.98e+02 ... (remaining 39943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18498 26.84 - 53.68: 411 53.68 - 80.52: 141 80.52 - 107.36: 123 107.36 - 134.20: 30 Dihedral angle restraints: 19203 sinusoidal: 9087 harmonic: 10116 Sorted by residual: dihedral pdb=" N CYS A 383 " pdb=" C CYS A 383 " pdb=" CA CYS A 383 " pdb=" CB CYS A 383 " ideal model delta harmonic sigma weight residual 122.80 96.18 26.62 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS B 383 " pdb=" C CYS B 383 " pdb=" CA CYS B 383 " pdb=" CB CYS B 383 " ideal model delta harmonic sigma weight residual 122.80 96.20 26.60 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS C 383 " pdb=" C CYS C 383 " pdb=" CA CYS C 383 " pdb=" CB CYS C 383 " ideal model delta harmonic sigma weight residual 122.80 96.20 26.60 0 2.50e+00 1.60e-01 1.13e+02 ... (remaining 19200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4787 0.390 - 0.780: 67 0.780 - 1.170: 6 1.170 - 1.560: 0 1.560 - 1.950: 3 Chirality restraints: 4863 Sorted by residual: 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 2.84 -0.44 2.00e-02 2.50e+03 4.89e+02 chirality pdb=" C1 MAN g 5 " pdb=" O6 BMA g 3 " pdb=" C2 MAN g 5 " pdb=" O5 MAN g 5 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-02 2.50e+03 4.73e+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 2.82 -0.42 2.00e-02 2.50e+03 4.43e+02 ... (remaining 4860 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " -0.078 2.00e-02 2.50e+03 4.33e-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 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.078 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 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 777 " 0.078 2.00e-02 2.50e+03 4.31e-02 3.72e+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 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7494 2.78 - 3.31: 26130 3.31 - 3.84: 51740 3.84 - 4.37: 63445 4.37 - 4.90: 101794 Nonbonded interactions: 250603 Sorted by model distance: nonbonded pdb=" O5 BMA g 3 " pdb=" O6 BMA g 3 " model vdw 2.255 2.432 nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.256 2.432 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.346 3.120 nonbonded pdb=" N ASP B 343 " pdb=" OD1 ASP B 343 " model vdw 2.346 3.120 ... (remaining 250598 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' selection = chain 'H' selection = chain 'O' selection = chain 'S' selection = chain 'Z' selection = chain 'd' } 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' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.010 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.120 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 29532 Z= 1.383 Angle : 2.054 25.286 40446 Z= 1.282 Chirality : 0.148 1.950 4863 Planarity : 0.009 0.048 4971 Dihedral : 15.855 134.197 12594 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.91 % Allowed : 1.31 % Favored : 97.78 % Cbeta Deviations : 0.65 % 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: -0.50 (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 C 190 TYR 0.079 0.011 TYR C 184 PHE 0.049 0.006 PHE B 473 TRP 0.019 0.005 TRP A1184 HIS 0.009 0.003 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.02529 (29349) covalent geometry : angle 2.02195 (39948) SS BOND : bond 0.04870 ( 51) SS BOND : angle 3.43272 ( 102) hydrogen bonds : bond 0.15184 ( 1157) hydrogen bonds : angle 7.72083 ( 3024) link_ALPHA1-2 : bond 0.06667 ( 6) link_ALPHA1-2 : angle 3.35695 ( 18) link_ALPHA1-3 : bond 0.05915 ( 15) link_ALPHA1-3 : angle 3.76423 ( 45) link_ALPHA1-6 : bond 0.05014 ( 9) link_ALPHA1-6 : angle 10.22142 ( 27) link_BETA1-4 : bond 0.06241 ( 48) link_BETA1-4 : angle 2.96172 ( 144) link_BETA2-3 : bond 0.01469 ( 3) link_BETA2-3 : angle 4.47227 ( 9) link_NAG-ASN : bond 0.03209 ( 51) link_NAG-ASN : angle 2.66904 ( 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 647 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 620 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 614 ARG cc_start: 0.6892 (mtm110) cc_final: 0.6655 (mtm110) REVERT: A 641 TYR cc_start: 0.8031 (t80) cc_final: 0.7651 (t80) REVERT: B 792 GLN cc_start: 0.8587 (mt0) cc_final: 0.8300 (mt0) REVERT: B 944 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6972 (pt0) outliers start: 27 outliers final: 4 residues processed: 635 average time/residue: 0.6532 time to fit residues: 483.9789 Evaluate side-chains 334 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 330 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 655 VAL 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: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 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 107 GLN A 280 GLN A 346 GLN A 521 ASN A 812 ASN A1028 ASN A1056 GLN A1063 GLN A1084 GLN A1097 GLN A1163 ASN A1208 GLN B 60 GLN B 261 GLN B 280 GLN B 346 GLN B 521 ASN B 812 ASN B 987 GLN B1056 GLN B1063 GLN B1084 GLN B1163 ASN B1169 ASN B1208 GLN C 280 GLN C 521 ASN C 765 ASN C 792 GLN C 808 GLN C1056 GLN C1084 GLN C1097 GLN C1163 ASN C1169 ASN C1208 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131431 restraints weight = 33494.749| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.83 r_work: 0.3337 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29532 Z= 0.198 Angle : 0.794 18.106 40446 Z= 0.389 Chirality : 0.052 0.655 4863 Planarity : 0.004 0.038 4971 Dihedral : 13.317 115.396 6570 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.92 % Allowed : 8.33 % Favored : 88.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.60 (0.14), residues: 3447 helix: 0.61 (0.20), residues: 708 sheet: 0.46 (0.16), residues: 846 loop : 0.44 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 269 TYR 0.021 0.002 TYR B 77 PHE 0.014 0.002 PHE C 850 TRP 0.008 0.001 TRP C 310 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00437 (29349) covalent geometry : angle 0.72190 (39948) SS BOND : bond 0.00615 ( 51) SS BOND : angle 1.31286 ( 102) hydrogen bonds : bond 0.05448 ( 1157) hydrogen bonds : angle 6.19805 ( 3024) link_ALPHA1-2 : bond 0.00483 ( 6) link_ALPHA1-2 : angle 1.67278 ( 18) link_ALPHA1-3 : bond 0.00911 ( 15) link_ALPHA1-3 : angle 2.43706 ( 45) link_ALPHA1-6 : bond 0.00664 ( 9) link_ALPHA1-6 : angle 1.89038 ( 27) link_BETA1-4 : bond 0.00979 ( 48) link_BETA1-4 : angle 3.09185 ( 144) link_BETA2-3 : bond 0.00809 ( 3) link_BETA2-3 : angle 1.42517 ( 9) link_NAG-ASN : bond 0.00855 ( 51) link_NAG-ASN : angle 4.18999 ( 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 485 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 398 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: A 473 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: A 944 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7485 (pt0) REVERT: A 988 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: A 1137 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: B 191 SER cc_start: 0.8154 (p) cc_final: 0.7797 (m) REVERT: B 238 THR cc_start: 0.8546 (p) cc_final: 0.8317 (m) REVERT: B 614 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.8079 (mtp-110) REVERT: B 728 LYS cc_start: 0.8373 (mptp) cc_final: 0.7780 (pmmt) REVERT: B 793 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 907 GLN cc_start: 0.7836 (pt0) cc_final: 0.7509 (pt0) REVERT: B 944 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7310 (pt0) REVERT: B 1137 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: C 191 SER cc_start: 0.8124 (p) cc_final: 0.7842 (m) REVERT: C 346 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 605 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 777 TYR cc_start: 0.8036 (m-80) cc_final: 0.7749 (m-80) outliers start: 87 outliers final: 27 residues processed: 446 average time/residue: 0.5925 time to fit residues: 314.9454 Evaluate side-chains 348 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 334 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 0.0770 chunk 227 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 107 GLN A 346 GLN A 466 GLN A 681 HIS A 765 ASN A 927 GLN A1056 GLN A1084 GLN A1163 ASN B 72 GLN B 346 GLN B 637 ASN B 681 HIS B 927 GLN B1028 ASN B1056 GLN B1145 ASN B1163 ASN C 637 ASN C 681 HIS C 765 ASN C 907 GLN C1056 GLN C1084 GLN C1097 GLN C1145 ASN C1163 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128521 restraints weight = 33535.947| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.79 r_work: 0.3303 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29532 Z= 0.186 Angle : 0.708 14.814 40446 Z= 0.345 Chirality : 0.049 0.446 4863 Planarity : 0.004 0.041 4971 Dihedral : 11.061 93.321 6567 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.72 % Allowed : 10.22 % Favored : 87.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.55 (0.14), residues: 3447 helix: 0.95 (0.20), residues: 714 sheet: 0.45 (0.17), residues: 807 loop : 0.23 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 614 TYR 0.018 0.002 TYR B 77 PHE 0.016 0.002 PHE C 850 TRP 0.007 0.001 TRP C 310 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00414 (29349) covalent geometry : angle 0.64561 (39948) SS BOND : bond 0.00711 ( 51) SS BOND : angle 1.36652 ( 102) hydrogen bonds : bond 0.04918 ( 1157) hydrogen bonds : angle 5.81526 ( 3024) link_ALPHA1-2 : bond 0.00554 ( 6) link_ALPHA1-2 : angle 1.59570 ( 18) link_ALPHA1-3 : bond 0.01118 ( 15) link_ALPHA1-3 : angle 1.53004 ( 45) link_ALPHA1-6 : bond 0.00799 ( 9) link_ALPHA1-6 : angle 1.75000 ( 27) link_BETA1-4 : bond 0.01078 ( 48) link_BETA1-4 : angle 2.61995 ( 144) link_BETA2-3 : bond 0.00852 ( 3) link_BETA2-3 : angle 1.58819 ( 9) link_NAG-ASN : bond 0.01228 ( 51) link_NAG-ASN : angle 3.78566 ( 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 449 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 368 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 SER cc_start: 0.8172 (p) cc_final: 0.7852 (m) REVERT: A 373 SER cc_start: 0.8439 (p) cc_final: 0.8221 (m) REVERT: A 473 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: A 605 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7707 (mm-30) REVERT: A 1203 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8677 (pttm) REVERT: B 191 SER cc_start: 0.8368 (p) cc_final: 0.8039 (m) REVERT: B 502 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7940 (tmmm) REVERT: B 537 ASP cc_start: 0.8027 (t70) cc_final: 0.7429 (m-30) REVERT: B 728 LYS cc_start: 0.8466 (mptp) cc_final: 0.7786 (pmmt) REVERT: B 793 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: B 818 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8433 (mt-10) REVERT: B 1068 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7568 (t70) REVERT: C 20 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7104 (t70) REVERT: C 191 SER cc_start: 0.8194 (p) cc_final: 0.7975 (m) REVERT: C 346 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: C 605 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7620 (mm-30) REVERT: C 607 SER cc_start: 0.8578 (t) cc_final: 0.8370 (m) REVERT: C 777 TYR cc_start: 0.8112 (m-80) cc_final: 0.7887 (m-80) REVERT: C 1031 GLN cc_start: 0.8051 (mt0) cc_final: 0.7802 (mp-120) outliers start: 81 outliers final: 34 residues processed: 416 average time/residue: 0.6121 time to fit residues: 301.9614 Evaluate side-chains 353 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 253 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 637 ASN A 681 HIS A 765 ASN A1056 GLN A1084 GLN A1163 ASN B 60 GLN B 98 GLN B 346 GLN B 681 HIS B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 261 GLN C 681 HIS C 765 ASN C 836 HIS C1056 GLN C1097 GLN C1119 GLN C1163 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126361 restraints weight = 33528.965| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.86 r_work: 0.3264 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29532 Z= 0.189 Angle : 0.694 13.949 40446 Z= 0.339 Chirality : 0.049 0.468 4863 Planarity : 0.004 0.041 4971 Dihedral : 9.439 86.111 6567 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.06 % Allowed : 10.58 % Favored : 86.36 % 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: 0.42 (0.14), residues: 3447 helix: 0.96 (0.20), residues: 705 sheet: 0.30 (0.17), residues: 834 loop : 0.12 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 141 TYR 0.017 0.002 TYR B 184 PHE 0.016 0.002 PHE C 827 TRP 0.006 0.001 TRP B1184 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00432 (29349) covalent geometry : angle 0.63716 (39948) SS BOND : bond 0.00617 ( 51) SS BOND : angle 1.66085 ( 102) hydrogen bonds : bond 0.04718 ( 1157) hydrogen bonds : angle 5.71252 ( 3024) link_ALPHA1-2 : bond 0.00449 ( 6) link_ALPHA1-2 : angle 1.64451 ( 18) link_ALPHA1-3 : bond 0.01075 ( 15) link_ALPHA1-3 : angle 1.89420 ( 45) link_ALPHA1-6 : bond 0.01013 ( 9) link_ALPHA1-6 : angle 1.61631 ( 27) link_BETA1-4 : bond 0.00916 ( 48) link_BETA1-4 : angle 2.36148 ( 144) link_BETA2-3 : bond 0.00674 ( 3) link_BETA2-3 : angle 1.21344 ( 9) link_NAG-ASN : bond 0.00933 ( 51) link_NAG-ASN : angle 3.51789 ( 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 439 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 348 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: A 191 SER cc_start: 0.8238 (p) cc_final: 0.7955 (m) REVERT: A 319 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (mp10) REVERT: A 473 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: A 605 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7671 (mm-30) REVERT: A 1024 ASP cc_start: 0.7258 (m-30) cc_final: 0.7002 (m-30) REVERT: A 1137 MET cc_start: 0.9004 (mtm) cc_final: 0.8725 (mtm) REVERT: A 1203 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8753 (pttm) REVERT: B 191 SER cc_start: 0.8451 (p) cc_final: 0.8153 (m) REVERT: B 502 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7984 (tmmm) REVERT: B 728 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7758 (pmmt) REVERT: B 793 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: B 818 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8277 (mt-10) REVERT: B 1035 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7982 (tttm) REVERT: B 1068 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7697 (t70) REVERT: B 1137 MET cc_start: 0.9145 (mtm) cc_final: 0.8932 (mpp) REVERT: C 346 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: C 605 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7728 (mm-30) REVERT: C 777 TYR cc_start: 0.8233 (m-80) cc_final: 0.8005 (m-80) REVERT: C 841 ARG cc_start: 0.8183 (tpt-90) cc_final: 0.7973 (tpt-90) REVERT: C 941 VAL cc_start: 0.8623 (t) cc_final: 0.8399 (m) REVERT: C 1024 ASP cc_start: 0.7230 (m-30) cc_final: 0.6997 (m-30) REVERT: C 1031 GLN cc_start: 0.7959 (mt0) cc_final: 0.7750 (mp10) REVERT: C 1216 THR cc_start: 0.7990 (p) cc_final: 0.7733 (t) outliers start: 91 outliers final: 40 residues processed: 400 average time/residue: 0.6214 time to fit residues: 294.8545 Evaluate side-chains 369 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 91 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 153 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 346 GLN A 681 HIS A 765 ASN A1056 GLN A1163 ASN B 60 GLN B 346 GLN B 836 HIS B1056 GLN B1163 ASN B1169 ASN C 765 ASN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126101 restraints weight = 33422.243| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.86 r_work: 0.3256 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29532 Z= 0.192 Angle : 0.693 19.917 40446 Z= 0.337 Chirality : 0.048 0.595 4863 Planarity : 0.004 0.042 4971 Dihedral : 8.871 86.959 6567 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.02 % Allowed : 10.99 % Favored : 85.99 % 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: 0.36 (0.14), residues: 3447 helix: 1.01 (0.20), residues: 705 sheet: 0.29 (0.17), residues: 837 loop : 0.02 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 614 TYR 0.013 0.001 TYR B 184 PHE 0.018 0.002 PHE C 827 TRP 0.005 0.001 TRP C 310 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00441 (29349) covalent geometry : angle 0.63153 (39948) SS BOND : bond 0.00663 ( 51) SS BOND : angle 1.72718 ( 102) hydrogen bonds : bond 0.04642 ( 1157) hydrogen bonds : angle 5.66068 ( 3024) link_ALPHA1-2 : bond 0.00476 ( 6) link_ALPHA1-2 : angle 1.58642 ( 18) link_ALPHA1-3 : bond 0.01072 ( 15) link_ALPHA1-3 : angle 1.69086 ( 45) link_ALPHA1-6 : bond 0.00935 ( 9) link_ALPHA1-6 : angle 1.61895 ( 27) link_BETA1-4 : bond 0.00872 ( 48) link_BETA1-4 : angle 2.38354 ( 144) link_BETA2-3 : bond 0.00608 ( 3) link_BETA2-3 : angle 1.14740 ( 9) link_NAG-ASN : bond 0.01038 ( 51) link_NAG-ASN : angle 3.70707 ( 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 429 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 339 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: A 191 SER cc_start: 0.8243 (p) cc_final: 0.7944 (m) REVERT: A 319 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8687 (mp10) REVERT: A 357 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: A 473 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: A 605 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7741 (mm-30) REVERT: A 786 PHE cc_start: 0.8375 (p90) cc_final: 0.8159 (p90) REVERT: A 987 GLN cc_start: 0.7388 (tp40) cc_final: 0.7116 (tp40) REVERT: A 1059 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 1090 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: A 1203 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (pttm) REVERT: B 191 SER cc_start: 0.8409 (p) cc_final: 0.8119 (m) REVERT: B 450 LEU cc_start: 0.8821 (tp) cc_final: 0.8372 (mm) REVERT: B 502 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7988 (tmmm) REVERT: B 728 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7776 (pmmt) REVERT: B 793 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: B 807 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (tttp) REVERT: B 818 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8283 (mt-10) REVERT: B 1035 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8017 (tmtm) REVERT: B 1068 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7705 (t70) REVERT: B 1137 MET cc_start: 0.9198 (mtm) cc_final: 0.8962 (mpp) REVERT: B 1183 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: C 20 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7183 (t70) REVERT: C 346 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: C 513 GLU cc_start: 0.6456 (tt0) cc_final: 0.5972 (mt-10) REVERT: C 605 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7728 (mm-30) REVERT: C 607 SER cc_start: 0.8571 (t) cc_final: 0.8343 (m) REVERT: C 777 TYR cc_start: 0.8258 (m-80) cc_final: 0.8047 (m-80) REVERT: C 841 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7947 (tpt-90) REVERT: C 941 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8412 (m) outliers start: 90 outliers final: 38 residues processed: 391 average time/residue: 0.6264 time to fit residues: 290.5792 Evaluate side-chains 372 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 180 optimal weight: 3.9990 chunk 284 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 681 HIS A 765 ASN A 836 HIS A1056 GLN A1163 ASN B1056 GLN B1163 ASN B1169 ASN C 681 HIS C 765 ASN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126535 restraints weight = 33365.670| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.86 r_work: 0.3269 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29532 Z= 0.169 Angle : 0.686 24.231 40446 Z= 0.332 Chirality : 0.047 0.414 4863 Planarity : 0.004 0.041 4971 Dihedral : 8.416 87.742 6566 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.79 % Allowed : 11.69 % Favored : 85.52 % 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: 0.38 (0.14), residues: 3447 helix: 1.10 (0.20), residues: 705 sheet: 0.25 (0.17), residues: 867 loop : 0.03 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 614 TYR 0.011 0.001 TYR C 184 PHE 0.018 0.001 PHE C 827 TRP 0.006 0.001 TRP C 310 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00381 (29349) covalent geometry : angle 0.62102 (39948) SS BOND : bond 0.00696 ( 51) SS BOND : angle 1.99228 ( 102) hydrogen bonds : bond 0.04446 ( 1157) hydrogen bonds : angle 5.59898 ( 3024) link_ALPHA1-2 : bond 0.00476 ( 6) link_ALPHA1-2 : angle 1.57062 ( 18) link_ALPHA1-3 : bond 0.01030 ( 15) link_ALPHA1-3 : angle 1.70153 ( 45) link_ALPHA1-6 : bond 0.00953 ( 9) link_ALPHA1-6 : angle 1.61378 ( 27) link_BETA1-4 : bond 0.00871 ( 48) link_BETA1-4 : angle 2.23993 ( 144) link_BETA2-3 : bond 0.00503 ( 3) link_BETA2-3 : angle 0.94450 ( 9) link_NAG-ASN : bond 0.00899 ( 51) link_NAG-ASN : angle 3.83038 ( 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 427 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 344 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 191 SER cc_start: 0.8241 (p) cc_final: 0.7976 (m) REVERT: A 319 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: A 357 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: A 473 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: A 605 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7747 (mm-30) REVERT: A 987 GLN cc_start: 0.7401 (tp40) cc_final: 0.7116 (tp40) REVERT: A 1059 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: A 1203 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8747 (pttm) REVERT: B 155 ASN cc_start: 0.7744 (m-40) cc_final: 0.7333 (m110) REVERT: B 191 SER cc_start: 0.8360 (p) cc_final: 0.8097 (m) REVERT: B 450 LEU cc_start: 0.8805 (tp) cc_final: 0.8348 (mm) REVERT: B 728 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7779 (pmmt) REVERT: B 793 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: B 807 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8486 (tttp) REVERT: B 818 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 1035 LYS cc_start: 0.8336 (mmtm) cc_final: 0.8038 (tmtm) REVERT: B 1068 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7665 (t70) REVERT: B 1090 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7913 (pp20) REVERT: B 1216 THR cc_start: 0.8356 (p) cc_final: 0.8098 (t) REVERT: C 20 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7276 (t70) REVERT: C 346 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: C 605 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7744 (mm-30) REVERT: C 607 SER cc_start: 0.8553 (t) cc_final: 0.8323 (m) REVERT: C 758 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8111 (mtm180) REVERT: C 777 TYR cc_start: 0.8252 (m-80) cc_final: 0.8050 (m-80) REVERT: C 841 ARG cc_start: 0.8175 (tpt-90) cc_final: 0.7966 (tpt-90) REVERT: C 1008 MET cc_start: 0.7372 (ptm) cc_final: 0.7109 (ptm) REVERT: C 1216 THR cc_start: 0.7908 (p) cc_final: 0.7674 (t) outliers start: 83 outliers final: 43 residues processed: 397 average time/residue: 0.6241 time to fit residues: 295.1004 Evaluate side-chains 374 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 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 718 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 287 optimal weight: 7.9990 chunk 294 optimal weight: 0.5980 chunk 200 optimal weight: 0.0270 chunk 311 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 302 optimal weight: 0.0000 chunk 166 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 overall best weight: 0.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 346 GLN A 681 HIS A 765 ASN A1056 GLN A1163 ASN B 765 ASN B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 681 HIS C 733 GLN C 765 ASN C 819 GLN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126864 restraints weight = 33411.139| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.86 r_work: 0.3275 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29532 Z= 0.159 Angle : 0.670 22.901 40446 Z= 0.325 Chirality : 0.047 0.392 4863 Planarity : 0.004 0.041 4971 Dihedral : 8.039 88.643 6566 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.89 % Allowed : 11.90 % Favored : 85.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3447 helix: 1.03 (0.20), residues: 723 sheet: 0.23 (0.17), residues: 867 loop : 0.01 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 614 TYR 0.011 0.001 TYR C 184 PHE 0.024 0.001 PHE C 827 TRP 0.006 0.001 TRP C 310 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00358 (29349) covalent geometry : angle 0.60840 (39948) SS BOND : bond 0.00675 ( 51) SS BOND : angle 2.13550 ( 102) hydrogen bonds : bond 0.04335 ( 1157) hydrogen bonds : angle 5.54775 ( 3024) link_ALPHA1-2 : bond 0.00484 ( 6) link_ALPHA1-2 : angle 1.54358 ( 18) link_ALPHA1-3 : bond 0.00990 ( 15) link_ALPHA1-3 : angle 1.64590 ( 45) link_ALPHA1-6 : bond 0.00938 ( 9) link_ALPHA1-6 : angle 1.60275 ( 27) link_BETA1-4 : bond 0.00853 ( 48) link_BETA1-4 : angle 2.18263 ( 144) link_BETA2-3 : bond 0.00509 ( 3) link_BETA2-3 : angle 0.85492 ( 9) link_NAG-ASN : bond 0.00898 ( 51) link_NAG-ASN : angle 3.60360 ( 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 429 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 191 SER cc_start: 0.8264 (p) cc_final: 0.8013 (m) REVERT: A 319 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8705 (mp10) REVERT: A 357 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: A 473 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.6777 (m-80) REVERT: A 605 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7794 (mm-30) REVERT: A 987 GLN cc_start: 0.7395 (tp40) cc_final: 0.7126 (tp40) REVERT: A 1059 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: A 1090 GLU cc_start: 0.8176 (pt0) cc_final: 0.7732 (pt0) REVERT: A 1203 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8778 (pttm) REVERT: B 155 ASN cc_start: 0.7582 (m-40) cc_final: 0.7231 (m110) REVERT: B 191 SER cc_start: 0.8388 (p) cc_final: 0.8141 (m) REVERT: B 319 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: B 728 LYS cc_start: 0.8409 (mptp) cc_final: 0.7764 (pmmt) REVERT: B 793 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: B 807 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (tttp) REVERT: B 818 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8265 (mt-10) REVERT: B 1035 LYS cc_start: 0.8336 (mmtm) cc_final: 0.8057 (tmtm) REVERT: B 1068 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7619 (t70) REVERT: B 1090 GLU cc_start: 0.8260 (pt0) cc_final: 0.7945 (pp20) REVERT: C 20 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7357 (t70) REVERT: C 346 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8081 (tp-100) REVERT: C 513 GLU cc_start: 0.6366 (tt0) cc_final: 0.5936 (mt-10) REVERT: C 605 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7735 (mm-30) REVERT: C 607 SER cc_start: 0.8556 (t) cc_final: 0.8321 (m) REVERT: C 841 ARG cc_start: 0.8181 (tpt-90) cc_final: 0.7971 (tpt-90) REVERT: C 1008 MET cc_start: 0.7383 (ptm) cc_final: 0.7153 (ptm) outliers start: 86 outliers final: 44 residues processed: 400 average time/residue: 0.6129 time to fit residues: 292.0012 Evaluate side-chains 383 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 639 VAL 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 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 42 optimal weight: 0.7980 chunk 332 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 486 HIS A 681 HIS A 733 GLN A 765 ASN A 792 GLN A1056 GLN A1163 ASN B 60 GLN B 733 GLN B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 765 ASN C 819 GLN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126093 restraints weight = 33453.054| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.86 r_work: 0.3268 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29532 Z= 0.187 Angle : 0.703 23.142 40446 Z= 0.342 Chirality : 0.050 0.873 4863 Planarity : 0.004 0.062 4971 Dihedral : 7.994 88.644 6565 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.99 % Allowed : 12.00 % Favored : 85.01 % Cbeta Deviations : 0.12 % 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: 0.36 (0.14), residues: 3447 helix: 1.14 (0.20), residues: 702 sheet: 0.24 (0.17), residues: 837 loop : -0.00 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 614 TYR 0.011 0.001 TYR B 184 PHE 0.021 0.002 PHE C 827 TRP 0.008 0.001 TRP A 960 HIS 0.012 0.001 HIS B 766 Details of bonding type rmsd covalent geometry : bond 0.00428 (29349) covalent geometry : angle 0.64098 (39948) SS BOND : bond 0.00662 ( 51) SS BOND : angle 2.20535 ( 102) hydrogen bonds : bond 0.04487 ( 1157) hydrogen bonds : angle 5.57042 ( 3024) link_ALPHA1-2 : bond 0.00479 ( 6) link_ALPHA1-2 : angle 1.55560 ( 18) link_ALPHA1-3 : bond 0.00950 ( 15) link_ALPHA1-3 : angle 1.63858 ( 45) link_ALPHA1-6 : bond 0.00888 ( 9) link_ALPHA1-6 : angle 1.62054 ( 27) link_BETA1-4 : bond 0.00814 ( 48) link_BETA1-4 : angle 2.20364 ( 144) link_BETA2-3 : bond 0.00524 ( 3) link_BETA2-3 : angle 0.88992 ( 9) link_NAG-ASN : bond 0.00996 ( 51) link_NAG-ASN : angle 3.71666 ( 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 435 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 346 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 191 SER cc_start: 0.8288 (p) cc_final: 0.8036 (m) REVERT: A 319 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8707 (mp10) REVERT: A 357 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: A 473 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: A 486 HIS cc_start: 0.7607 (m-70) cc_final: 0.7369 (m90) REVERT: A 605 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7788 (mm-30) REVERT: A 786 PHE cc_start: 0.8161 (p90) cc_final: 0.7940 (p90) REVERT: A 793 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: A 987 GLN cc_start: 0.7409 (tp40) cc_final: 0.7160 (tp40) REVERT: A 1059 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: A 1203 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8780 (pttm) REVERT: B 155 ASN cc_start: 0.7537 (m-40) cc_final: 0.7196 (m110) REVERT: B 191 SER cc_start: 0.8421 (p) cc_final: 0.8179 (m) REVERT: B 319 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: B 450 LEU cc_start: 0.8798 (tp) cc_final: 0.8353 (mm) REVERT: B 728 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7814 (pmmt) REVERT: B 793 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: B 807 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (tttp) REVERT: B 818 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 1035 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8006 (tmtm) REVERT: B 1068 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7635 (t70) REVERT: B 1090 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: B 1183 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6554 (tt0) REVERT: B 1216 THR cc_start: 0.8411 (p) cc_final: 0.8176 (t) REVERT: C 20 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7341 (t70) REVERT: C 346 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: C 513 GLU cc_start: 0.6460 (tt0) cc_final: 0.6014 (mt-10) REVERT: C 605 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7713 (mm-30) REVERT: C 841 ARG cc_start: 0.8180 (tpt-90) cc_final: 0.7973 (tpt-90) REVERT: C 899 THR cc_start: 0.8725 (m) cc_final: 0.8492 (t) REVERT: C 1216 THR cc_start: 0.8069 (p) cc_final: 0.7855 (t) outliers start: 89 outliers final: 50 residues processed: 400 average time/residue: 0.6239 time to fit residues: 296.8295 Evaluate side-chains 393 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 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 718 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 272 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 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 346 GLN A 765 ASN A1056 GLN A1163 ASN B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 765 ASN C 819 GLN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126763 restraints weight = 33431.574| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.85 r_work: 0.3278 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29532 Z= 0.163 Angle : 0.685 21.737 40446 Z= 0.332 Chirality : 0.048 0.576 4863 Planarity : 0.004 0.061 4971 Dihedral : 7.768 89.208 6565 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 12.47 % Favored : 84.95 % 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: 0.35 (0.14), residues: 3447 helix: 1.15 (0.20), residues: 702 sheet: 0.23 (0.17), residues: 822 loop : -0.02 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 614 TYR 0.010 0.001 TYR B1141 PHE 0.019 0.001 PHE C 827 TRP 0.007 0.001 TRP A 960 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00365 (29349) covalent geometry : angle 0.61923 (39948) SS BOND : bond 0.00636 ( 51) SS BOND : angle 2.18689 ( 102) hydrogen bonds : bond 0.04310 ( 1157) hydrogen bonds : angle 5.54172 ( 3024) link_ALPHA1-2 : bond 0.00487 ( 6) link_ALPHA1-2 : angle 1.52984 ( 18) link_ALPHA1-3 : bond 0.00918 ( 15) link_ALPHA1-3 : angle 1.61280 ( 45) link_ALPHA1-6 : bond 0.00885 ( 9) link_ALPHA1-6 : angle 1.57564 ( 27) link_BETA1-4 : bond 0.00813 ( 48) link_BETA1-4 : angle 2.26880 ( 144) link_BETA2-3 : bond 0.00302 ( 3) link_BETA2-3 : angle 0.68175 ( 9) link_NAG-ASN : bond 0.01184 ( 51) link_NAG-ASN : angle 3.80241 ( 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 420 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 343 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 191 SER cc_start: 0.8231 (p) cc_final: 0.8007 (m) REVERT: A 319 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: A 357 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 473 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: A 605 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7817 (mm-30) REVERT: A 786 PHE cc_start: 0.8087 (p90) cc_final: 0.7868 (p90) REVERT: A 793 GLU cc_start: 0.8539 (tt0) cc_final: 0.8274 (tt0) REVERT: A 987 GLN cc_start: 0.7506 (tp40) cc_final: 0.7253 (tp40) REVERT: A 1059 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: A 1090 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: A 1203 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8761 (pttm) REVERT: B 155 ASN cc_start: 0.7544 (m-40) cc_final: 0.7222 (m110) REVERT: B 191 SER cc_start: 0.8428 (p) cc_final: 0.8203 (m) REVERT: B 319 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: B 450 LEU cc_start: 0.8796 (tp) cc_final: 0.8365 (mm) REVERT: B 605 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7865 (mm-30) REVERT: B 728 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7814 (pmmt) REVERT: B 793 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 807 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8245 (mttp) REVERT: B 818 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 853 VAL cc_start: 0.7881 (m) cc_final: 0.7652 (p) REVERT: B 1035 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8016 (tmtm) REVERT: B 1068 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7623 (t70) REVERT: B 1090 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: B 1183 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6176 (tp30) REVERT: C 20 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7329 (t70) REVERT: C 155 ASN cc_start: 0.7635 (m-40) cc_final: 0.7245 (m110) REVERT: C 346 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8083 (tp-100) REVERT: C 513 GLU cc_start: 0.6425 (tt0) cc_final: 0.6019 (mt-10) REVERT: C 605 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7711 (mm-30) REVERT: C 841 ARG cc_start: 0.8189 (tpt-90) cc_final: 0.7986 (tpt-90) REVERT: C 899 THR cc_start: 0.8714 (m) cc_final: 0.8500 (t) outliers start: 77 outliers final: 47 residues processed: 391 average time/residue: 0.6003 time to fit residues: 279.8176 Evaluate side-chains 386 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 639 VAL 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 1005 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 267 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 197 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A1056 GLN A1163 ASN B 60 GLN B 98 GLN B 346 GLN B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 765 ASN C 819 GLN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127448 restraints weight = 33277.365| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.86 r_work: 0.3302 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29532 Z= 0.149 Angle : 0.662 17.429 40446 Z= 0.323 Chirality : 0.046 0.395 4863 Planarity : 0.004 0.062 4971 Dihedral : 7.505 89.999 6565 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.35 % Allowed : 12.84 % 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: 0.40 (0.14), residues: 3447 helix: 1.18 (0.20), residues: 705 sheet: 0.28 (0.17), residues: 852 loop : -0.00 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 614 TYR 0.010 0.001 TYR C 909 PHE 0.018 0.001 PHE C 827 TRP 0.007 0.001 TRP A 960 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00332 (29349) covalent geometry : angle 0.60242 (39948) SS BOND : bond 0.00589 ( 51) SS BOND : angle 2.10323 ( 102) hydrogen bonds : bond 0.04169 ( 1157) hydrogen bonds : angle 5.49786 ( 3024) link_ALPHA1-2 : bond 0.00491 ( 6) link_ALPHA1-2 : angle 1.51432 ( 18) link_ALPHA1-3 : bond 0.00873 ( 15) link_ALPHA1-3 : angle 1.60401 ( 45) link_ALPHA1-6 : bond 0.00851 ( 9) link_ALPHA1-6 : angle 1.52908 ( 27) link_BETA1-4 : bond 0.00837 ( 48) link_BETA1-4 : angle 2.12411 ( 144) link_BETA2-3 : bond 0.00367 ( 3) link_BETA2-3 : angle 0.60254 ( 9) link_NAG-ASN : bond 0.01026 ( 51) link_NAG-ASN : angle 3.53375 ( 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 421 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 351 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: A 191 SER cc_start: 0.8200 (p) cc_final: 0.7991 (m) REVERT: A 319 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8690 (mp10) REVERT: A 357 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: A 473 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: A 605 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7845 (mm-30) REVERT: A 793 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: A 987 GLN cc_start: 0.7422 (tp40) cc_final: 0.7163 (tp40) REVERT: A 1009 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6726 (tp-100) REVERT: A 1059 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 1090 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: A 1203 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8767 (pttm) REVERT: B 155 ASN cc_start: 0.7572 (m-40) cc_final: 0.7227 (m110) REVERT: B 191 SER cc_start: 0.8442 (p) cc_final: 0.8228 (m) REVERT: B 319 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8666 (mp10) REVERT: B 725 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6309 (mt-10) REVERT: B 728 LYS cc_start: 0.8419 (mptp) cc_final: 0.7818 (pmmt) REVERT: B 793 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: B 853 VAL cc_start: 0.7778 (m) cc_final: 0.7538 (p) REVERT: B 899 THR cc_start: 0.8649 (m) cc_final: 0.8427 (p) REVERT: B 907 GLN cc_start: 0.7894 (pt0) cc_final: 0.7605 (mt0) REVERT: B 1035 LYS cc_start: 0.8340 (mmtm) cc_final: 0.8009 (tmtm) REVERT: B 1068 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: B 1090 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7998 (pp20) REVERT: C 155 ASN cc_start: 0.7579 (m-40) cc_final: 0.7157 (m110) REVERT: C 346 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8099 (tp-100) REVERT: C 513 GLU cc_start: 0.6397 (tt0) cc_final: 0.6031 (mt-10) REVERT: C 605 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7677 (mm-30) REVERT: C 841 ARG cc_start: 0.8185 (tpt-90) cc_final: 0.7979 (tpt-90) REVERT: C 1008 MET cc_start: 0.7407 (ptm) cc_final: 0.7100 (ptm) REVERT: C 1212 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8043 (mp-120) outliers start: 70 outliers final: 41 residues processed: 394 average time/residue: 0.5930 time to fit residues: 278.4493 Evaluate side-chains 382 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 328 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 167 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 344 optimal weight: 0.0070 chunk 280 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 342 optimal weight: 0.9990 chunk 318 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 765 ASN A1056 GLN A1097 GLN A1163 ASN B 346 GLN B1056 GLN B1163 ASN B1169 ASN C 98 GLN C 765 ASN C 819 GLN C1056 GLN C1097 GLN C1163 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128227 restraints weight = 33661.126| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.72 r_work: 0.3303 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29532 Z= 0.147 Angle : 0.663 24.033 40446 Z= 0.323 Chirality : 0.046 0.408 4863 Planarity : 0.004 0.060 4971 Dihedral : 7.406 89.938 6565 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.25 % Allowed : 13.17 % Favored : 84.58 % 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: 0.40 (0.14), residues: 3447 helix: 1.21 (0.20), residues: 705 sheet: 0.26 (0.17), residues: 819 loop : 0.01 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 614 TYR 0.010 0.001 TYR B1141 PHE 0.017 0.001 PHE C 827 TRP 0.008 0.001 TRP A 535 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00329 (29349) covalent geometry : angle 0.60524 (39948) SS BOND : bond 0.00692 ( 51) SS BOND : angle 2.15316 ( 102) hydrogen bonds : bond 0.04151 ( 1157) hydrogen bonds : angle 5.48198 ( 3024) link_ALPHA1-2 : bond 0.00491 ( 6) link_ALPHA1-2 : angle 1.50851 ( 18) link_ALPHA1-3 : bond 0.00836 ( 15) link_ALPHA1-3 : angle 1.60189 ( 45) link_ALPHA1-6 : bond 0.00826 ( 9) link_ALPHA1-6 : angle 1.50649 ( 27) link_BETA1-4 : bond 0.00815 ( 48) link_BETA1-4 : angle 2.09738 ( 144) link_BETA2-3 : bond 0.00286 ( 3) link_BETA2-3 : angle 0.54784 ( 9) link_NAG-ASN : bond 0.00954 ( 51) link_NAG-ASN : angle 3.45624 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11155.67 seconds wall clock time: 190 minutes 57.17 seconds (11457.17 seconds total)