Starting phenix.real_space_refine on Fri Mar 6 07:23:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q04_20542/03_2026/6q04_20542.map" } resolution = 2.5 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= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 18108 2.51 5 N 4533 2.21 5 O 6123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28911 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "B" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "C" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 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: "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: 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: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "e" 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: "f" 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: "g" 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: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Time building chain proxies: 6.52, per 1000 atoms: 0.23 Number of scatterers: 28911 At special positions: 0 Unit cell: (141.75, 150.15, 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 6123 8.00 N 4533 7.00 C 18108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.08 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.09 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.06 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.12 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.09 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.05 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.08 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.17 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.09 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.02 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.06 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.12 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.09 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.05 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.08 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.09 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.02 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.06 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.12 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.09 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 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 N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 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 N 1 " - " ASN B 222 " " NAG O 1 " - " ASN B 236 " " NAG P 1 " - " ASN B 410 " " NAG Q 1 " - " ASN B 870 " " NAG R 1 " - " ASN B1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 166 " " NAG W 1 " - " ASN B 244 " " NAG X 1 " - " ASN C 222 " " NAG Y 1 " - " ASN C 236 " " NAG Z 1 " - " ASN C 410 " " NAG a 1 " - " ASN C 870 " " NAG b 1 " - " ASN C1213 " " NAG c 1 " - " ASN C 66 " " NAG d 1 " - " ASN C 104 " " NAG e 1 " - " ASN C 125 " " NAG f 1 " - " ASN C 166 " " NAG g 1 " - " ASN C 244 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1444 " pdb=" CB FOL B1444 " pdb=" CB FOL C1444 " Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 57 sheets defined 27.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.679A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.853A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.773A 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: 3.918A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 596 through 600 removed outlier: 3.836A 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: 4.086A pdb=" N LEU B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.854A 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: 3.918A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.174A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.319A 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: 6.613A 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: 5.244A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.726A 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: 5.437A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.527A 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: 5.469A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 5.656A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.836A 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: 5.926A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.837A 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: 4.741A 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: 4.166A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.166A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.425A 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: 6.613A 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: 3.525A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.731A 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: 6.528A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.469A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1191 through 1195 removed outlier: 5.655A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B1188 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.610A 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: 4.165A 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: 5.244A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF5, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.863A 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: 3.524A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AF8, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.628A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.825A 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: 4.609A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 3.92 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: 4510 1.26 - 1.46: 12119 1.46 - 1.66: 12468 1.66 - 1.85: 216 Bond restraints: 29316 Sorted by residual: 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 9.08e+02 bond pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.08e+02 bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.05e+02 bond pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 bond pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 ... (remaining 29311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 38422 4.37 - 8.74: 1330 8.74 - 13.11: 100 13.11 - 17.48: 21 17.48 - 21.85: 33 Bond angle restraints: 39906 Sorted by residual: angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.20 -21.28 1.15e+00 7.56e-01 3.42e+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 94.48 21.38 1.24e+00 6.50e-01 2.97e+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 94.49 21.37 1.24e+00 6.50e-01 2.97e+02 ... (remaining 39901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18444 26.84 - 53.67: 405 53.67 - 80.51: 138 80.51 - 107.34: 131 107.34 - 134.18: 31 Dihedral angle restraints: 19149 sinusoidal: 9033 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 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 96.19 26.61 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 96.19 26.61 0 2.50e+00 1.60e-01 1.13e+02 ... (remaining 19146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4771 0.390 - 0.781: 68 0.781 - 1.171: 6 1.171 - 1.561: 0 1.561 - 1.952: 3 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 MAN U 5 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 5 " pdb=" O5 MAN U 5 " both_signs ideal model delta sigma weight residual False 2.40 2.85 -0.45 2.00e-02 2.50e+03 4.96e+02 chirality pdb=" C1 MAN e 4 " pdb=" O3 BMA e 3 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 2.84 -0.44 2.00e-02 2.50e+03 4.80e+02 chirality pdb=" C1 MAN K 5 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 5 " pdb=" O5 MAN K 5 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-02 2.50e+03 4.72e+02 ... (remaining 4845 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 4.34e-02 3.76e+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 " 0.028 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 3.73e+01 pdb=" CG TYR B 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.028 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 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7506 2.78 - 3.31: 26115 3.31 - 3.84: 51776 3.84 - 4.37: 63392 4.37 - 4.90: 101827 Nonbonded interactions: 250616 Sorted by model distance: nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA U 3 " pdb=" O6 BMA U 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA e 3 " pdb=" O6 BMA e 3 " model vdw 2.256 2.432 nonbonded pdb=" N ASP B 343 " pdb=" OD1 ASP B 343 " model vdw 2.345 3.120 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.346 3.120 ... (remaining 250611 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 'N' selection = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'U' selection = chain 'V' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 29.470 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 29496 Z= 1.384 Angle : 2.053 25.937 40395 Z= 1.283 Chirality : 0.148 1.952 4848 Planarity : 0.009 0.048 4971 Dihedral : 15.995 134.180 12540 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.91 % Allowed : 1.31 % Favored : 97.78 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 3447 helix: -0.49 (0.17), residues: 678 sheet: 0.67 (0.17), residues: 846 loop : 0.78 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 190 TYR 0.079 0.011 TYR A 184 PHE 0.050 0.006 PHE B 473 TRP 0.019 0.005 TRP A1184 HIS 0.009 0.003 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.02530 (29316) covalent geometry : angle 2.02009 (39906) SS BOND : bond 0.04853 ( 51) SS BOND : angle 3.43679 ( 102) hydrogen bonds : bond 0.15185 ( 1157) hydrogen bonds : angle 7.71982 ( 3024) link_ALPHA1-2 : bond 0.06670 ( 6) link_ALPHA1-2 : angle 3.34714 ( 18) link_ALPHA1-3 : bond 0.06000 ( 15) link_ALPHA1-3 : angle 3.69857 ( 45) link_ALPHA1-6 : bond 0.05256 ( 9) link_ALPHA1-6 : angle 10.66529 ( 27) link_BETA1-4 : bond 0.06237 ( 48) link_BETA1-4 : angle 2.96214 ( 144) link_NAG-ASN : bond 0.03216 ( 51) link_NAG-ASN : angle 2.66657 ( 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 617 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 590 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8324 (pt) cc_final: 0.8104 (pt) outliers start: 27 outliers final: 4 residues processed: 605 average time/residue: 0.6543 time to fit residues: 462.6450 Evaluate side-chains 325 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 321 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 107 GLN A 280 GLN A 521 ASN A 576 GLN A 582 ASN A 681 HIS ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN A1072 ASN A1163 ASN B 107 GLN B 280 GLN B 576 GLN B 582 ASN B 681 HIS B 819 GLN B 832 ASN B 987 GLN B 988 GLN B 994 GLN B1072 ASN C 107 GLN C 280 GLN C 304 GLN C 521 ASN C 582 ASN C 812 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.156164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122410 restraints weight = 33000.269| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.35 r_work: 0.3375 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29496 Z= 0.195 Angle : 0.768 15.699 40395 Z= 0.383 Chirality : 0.051 0.820 4848 Planarity : 0.004 0.037 4971 Dihedral : 13.361 116.561 6518 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.45 % Allowed : 10.11 % Favored : 87.43 % 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: 0.66 (0.14), residues: 3447 helix: 0.67 (0.20), residues: 693 sheet: 0.53 (0.16), residues: 846 loop : 0.46 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 141 TYR 0.023 0.002 TYR A 77 PHE 0.023 0.002 PHE B 850 TRP 0.010 0.001 TRP B 310 HIS 0.008 0.001 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.00427 (29316) covalent geometry : angle 0.71389 (39906) SS BOND : bond 0.00680 ( 51) SS BOND : angle 1.25652 ( 102) hydrogen bonds : bond 0.05592 ( 1157) hydrogen bonds : angle 6.14591 ( 3024) link_ALPHA1-2 : bond 0.00366 ( 6) link_ALPHA1-2 : angle 1.70513 ( 18) link_ALPHA1-3 : bond 0.00934 ( 15) link_ALPHA1-3 : angle 2.26196 ( 45) link_ALPHA1-6 : bond 0.00607 ( 9) link_ALPHA1-6 : angle 2.04560 ( 27) link_BETA1-4 : bond 0.00846 ( 48) link_BETA1-4 : angle 3.01823 ( 144) link_NAG-ASN : bond 0.00667 ( 51) link_NAG-ASN : angle 3.23775 ( 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 482 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 409 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 487 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.5298 (t0) REVERT: A 587 LYS cc_start: 0.7604 (ptpp) cc_final: 0.7282 (mptt) REVERT: A 600 LEU cc_start: 0.8623 (mt) cc_final: 0.8262 (mm) REVERT: A 614 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7413 (mtt180) REVERT: A 666 GLU cc_start: 0.7844 (mp0) cc_final: 0.7511 (mp0) REVERT: A 899 THR cc_start: 0.7924 (m) cc_final: 0.7569 (p) REVERT: A 913 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5362 (mmt) REVERT: A 1068 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7977 (t70) REVERT: A 1137 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7945 (mtm) REVERT: B 141 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7119 (mtp180) REVERT: B 369 LYS cc_start: 0.6250 (mptt) cc_final: 0.5979 (mptt) REVERT: B 379 GLU cc_start: 0.7148 (tt0) cc_final: 0.6650 (mm-30) REVERT: B 536 GLU cc_start: 0.6983 (pp20) cc_final: 0.6653 (pp20) REVERT: B 587 LYS cc_start: 0.7378 (ptpp) cc_final: 0.7081 (mptt) REVERT: B 764 PHE cc_start: 0.8232 (t80) cc_final: 0.7862 (t80) REVERT: B 854 LYS cc_start: 0.6748 (tttm) cc_final: 0.6156 (tptp) REVERT: B 909 TYR cc_start: 0.7787 (t80) cc_final: 0.7472 (t80) REVERT: B 1035 LYS cc_start: 0.7940 (mptt) cc_final: 0.7204 (tttm) REVERT: B 1061 PRO cc_start: 0.7037 (Cg_endo) cc_final: 0.6635 (Cg_exo) REVERT: B 1062 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6597 (mp0) REVERT: B 1105 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: B 1113 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7797 (mtp180) REVERT: B 1148 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: C 141 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7086 (mtp180) REVERT: C 352 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8064 (mt-10) REVERT: C 406 ASN cc_start: 0.7916 (m-40) cc_final: 0.7655 (m-40) REVERT: C 536 GLU cc_start: 0.6758 (pp20) cc_final: 0.6512 (pp20) REVERT: C 587 LYS cc_start: 0.7350 (ptpp) cc_final: 0.7104 (mptt) REVERT: C 614 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7582 (mtt180) REVERT: C 666 GLU cc_start: 0.7683 (mp0) cc_final: 0.7416 (mp0) REVERT: C 777 TYR cc_start: 0.7942 (m-80) cc_final: 0.7615 (m-80) REVERT: C 826 GLN cc_start: 0.6685 (mm110) cc_final: 0.6421 (mm-40) REVERT: C 854 LYS cc_start: 0.6946 (tttm) cc_final: 0.6261 (tptm) REVERT: C 862 ILE cc_start: 0.6971 (pt) cc_final: 0.6596 (mp) REVERT: C 875 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7195 (mt-10) REVERT: C 899 THR cc_start: 0.8070 (m) cc_final: 0.7662 (p) REVERT: C 1031 GLN cc_start: 0.7726 (mm110) cc_final: 0.7520 (mm110) REVERT: C 1056 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 1137 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7976 (mtm) outliers start: 73 outliers final: 19 residues processed: 450 average time/residue: 0.6239 time to fit residues: 330.9564 Evaluate side-chains 343 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 466 GLN A 647 ASN A 681 HIS A 832 ASN B 466 GLN B 647 ASN B 681 HIS ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B 987 GLN C 261 GLN C 466 GLN C 987 GLN C1145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116940 restraints weight = 32865.284| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.31 r_work: 0.3301 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 29496 Z= 0.278 Angle : 0.805 16.537 40395 Z= 0.398 Chirality : 0.051 0.353 4848 Planarity : 0.005 0.054 4971 Dihedral : 11.493 95.940 6510 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.60 % Allowed : 11.29 % Favored : 85.11 % 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: 0.72 (0.20), residues: 702 sheet: 0.34 (0.17), residues: 810 loop : 0.12 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.022 0.002 TYR A 77 PHE 0.024 0.002 PHE C 473 TRP 0.010 0.002 TRP B 310 HIS 0.009 0.002 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00657 (29316) covalent geometry : angle 0.75257 (39906) SS BOND : bond 0.00932 ( 51) SS BOND : angle 2.72122 ( 102) hydrogen bonds : bond 0.05652 ( 1157) hydrogen bonds : angle 6.04750 ( 3024) link_ALPHA1-2 : bond 0.00695 ( 6) link_ALPHA1-2 : angle 1.54850 ( 18) link_ALPHA1-3 : bond 0.01075 ( 15) link_ALPHA1-3 : angle 1.73367 ( 45) link_ALPHA1-6 : bond 0.00612 ( 9) link_ALPHA1-6 : angle 1.71277 ( 27) link_BETA1-4 : bond 0.00918 ( 48) link_BETA1-4 : angle 2.67335 ( 144) link_NAG-ASN : bond 0.00796 ( 51) link_NAG-ASN : angle 3.18487 ( 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 460 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 353 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8200 (mmmm) REVERT: A 303 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7532 (pp) REVERT: A 487 ASN cc_start: 0.4995 (OUTLIER) cc_final: 0.4656 (t0) REVERT: A 542 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7874 (mtt90) REVERT: A 548 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7175 (mt) REVERT: A 600 LEU cc_start: 0.8675 (mt) cc_final: 0.8336 (mm) REVERT: A 614 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7582 (mtt90) REVERT: A 666 GLU cc_start: 0.7842 (mp0) cc_final: 0.7502 (mp0) REVERT: A 856 SER cc_start: 0.8749 (t) cc_final: 0.8483 (p) REVERT: A 899 THR cc_start: 0.7966 (m) cc_final: 0.7639 (p) REVERT: A 913 MET cc_start: 0.5775 (mtt) cc_final: 0.5314 (mmt) REVERT: A 988 GLN cc_start: 0.7836 (tt0) cc_final: 0.7626 (tt0) REVERT: A 995 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7430 (mmmt) REVERT: A 1068 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7922 (t70) REVERT: A 1137 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: A 1148 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 141 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7116 (mtp85) REVERT: B 352 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8099 (mm-30) REVERT: B 379 GLU cc_start: 0.7151 (tt0) cc_final: 0.6748 (mm-30) REVERT: B 536 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: B 600 LEU cc_start: 0.8520 (mt) cc_final: 0.8100 (mm) REVERT: B 777 TYR cc_start: 0.8086 (m-80) cc_final: 0.7482 (m-10) REVERT: B 796 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: B 899 THR cc_start: 0.7970 (m) cc_final: 0.7608 (p) REVERT: B 909 TYR cc_start: 0.7958 (t80) cc_final: 0.7635 (t80) REVERT: B 1035 LYS cc_start: 0.7936 (mptt) cc_final: 0.7239 (tttm) REVERT: B 1062 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 1105 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 1137 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8147 (ttp) REVERT: B 1148 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: C 31 ILE cc_start: 0.8118 (mt) cc_final: 0.7867 (mp) REVERT: C 141 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7054 (mtp180) REVERT: C 252 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6910 (pt0) REVERT: C 400 LYS cc_start: 0.8383 (mttm) cc_final: 0.8148 (mttp) REVERT: C 406 ASN cc_start: 0.7845 (m-40) cc_final: 0.7519 (m-40) REVERT: C 536 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6497 (pp20) REVERT: C 777 TYR cc_start: 0.8153 (m-80) cc_final: 0.7778 (m-80) REVERT: C 812 ASN cc_start: 0.8555 (t0) cc_final: 0.8301 (t160) REVERT: C 815 GLN cc_start: 0.7271 (mp10) cc_final: 0.6882 (tp-100) REVERT: C 818 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: C 842 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: C 854 LYS cc_start: 0.7109 (tttm) cc_final: 0.6370 (tptp) REVERT: C 899 THR cc_start: 0.8245 (m) cc_final: 0.7847 (p) REVERT: C 1035 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7488 (tttm) REVERT: C 1056 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7778 (tt0) outliers start: 107 outliers final: 50 residues processed: 415 average time/residue: 0.5485 time to fit residues: 273.9401 Evaluate side-chains 370 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1162 THR 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 22 optimal weight: 0.0270 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 262 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 812 ASN A 832 ASN B 194 HIS B 681 HIS B 812 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN C 194 HIS C 261 GLN C1169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120210 restraints weight = 32818.790| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.32 r_work: 0.3345 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29496 Z= 0.151 Angle : 0.690 22.207 40395 Z= 0.336 Chirality : 0.047 0.415 4848 Planarity : 0.004 0.044 4971 Dihedral : 9.386 80.032 6510 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.16 % Allowed : 12.70 % Favored : 84.14 % 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: 0.38 (0.14), residues: 3447 helix: 1.01 (0.20), residues: 702 sheet: 0.25 (0.17), residues: 864 loop : 0.08 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 141 TYR 0.012 0.001 TYR A 909 PHE 0.022 0.001 PHE A 473 TRP 0.008 0.001 TRP B 310 HIS 0.006 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00332 (29316) covalent geometry : angle 0.63543 (39906) SS BOND : bond 0.00750 ( 51) SS BOND : angle 2.51270 ( 102) hydrogen bonds : bond 0.04575 ( 1157) hydrogen bonds : angle 5.77877 ( 3024) link_ALPHA1-2 : bond 0.00555 ( 6) link_ALPHA1-2 : angle 1.57983 ( 18) link_ALPHA1-3 : bond 0.01146 ( 15) link_ALPHA1-3 : angle 1.89176 ( 45) link_ALPHA1-6 : bond 0.00855 ( 9) link_ALPHA1-6 : angle 1.55228 ( 27) link_BETA1-4 : bond 0.00899 ( 48) link_BETA1-4 : angle 2.33996 ( 144) link_NAG-ASN : bond 0.00588 ( 51) link_NAG-ASN : angle 3.06091 ( 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 444 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 350 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 303 ILE cc_start: 0.8109 (pt) cc_final: 0.7762 (pp) REVERT: A 487 ASN cc_start: 0.5163 (OUTLIER) cc_final: 0.4505 (t0) REVERT: A 542 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7905 (mtt90) REVERT: A 548 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7128 (mt) REVERT: A 600 LEU cc_start: 0.8668 (mt) cc_final: 0.8347 (mm) REVERT: A 614 ARG cc_start: 0.7955 (mtt90) cc_final: 0.7593 (mtt90) REVERT: A 666 GLU cc_start: 0.7875 (mp0) cc_final: 0.7566 (mp0) REVERT: A 764 PHE cc_start: 0.8233 (t80) cc_final: 0.7964 (t80) REVERT: A 856 SER cc_start: 0.8732 (t) cc_final: 0.8473 (p) REVERT: A 899 THR cc_start: 0.8024 (m) cc_final: 0.7724 (p) REVERT: A 906 MET cc_start: 0.8311 (ttp) cc_final: 0.8078 (ttm) REVERT: A 913 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5285 (mmt) REVERT: A 988 GLN cc_start: 0.7851 (tt0) cc_final: 0.7599 (tt0) REVERT: A 995 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7347 (mmmt) REVERT: A 1035 LYS cc_start: 0.7884 (mptt) cc_final: 0.7108 (ttpt) REVERT: A 1068 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7926 (t70) REVERT: A 1137 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8176 (mtp) REVERT: A 1148 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 141 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7172 (mtp180) REVERT: B 352 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8172 (mm-30) REVERT: B 379 GLU cc_start: 0.7144 (tt0) cc_final: 0.6770 (mm-30) REVERT: B 381 VAL cc_start: 0.8042 (m) cc_final: 0.7678 (p) REVERT: B 536 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6709 (pp20) REVERT: B 600 LEU cc_start: 0.8437 (mt) cc_final: 0.8085 (mm) REVERT: B 764 PHE cc_start: 0.8424 (t80) cc_final: 0.8161 (t80) REVERT: B 777 TYR cc_start: 0.8080 (m-80) cc_final: 0.7466 (m-10) REVERT: B 899 THR cc_start: 0.7847 (m) cc_final: 0.7492 (p) REVERT: B 909 TYR cc_start: 0.8047 (t80) cc_final: 0.7666 (t80) REVERT: B 1035 LYS cc_start: 0.7868 (mptt) cc_final: 0.7223 (tttm) REVERT: B 1062 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: B 1105 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: B 1148 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: C 31 ILE cc_start: 0.8078 (mt) cc_final: 0.7808 (mp) REVERT: C 98 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: C 141 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7120 (mtp85) REVERT: C 252 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: C 406 ASN cc_start: 0.7742 (m-40) cc_final: 0.7418 (m-40) REVERT: C 536 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: C 614 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7592 (mtt180) REVERT: C 777 TYR cc_start: 0.8098 (m-80) cc_final: 0.7687 (m-80) REVERT: C 812 ASN cc_start: 0.8529 (t0) cc_final: 0.8325 (t160) REVERT: C 815 GLN cc_start: 0.7271 (mp10) cc_final: 0.6819 (tp-100) REVERT: C 818 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: C 842 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: C 854 LYS cc_start: 0.7158 (tttm) cc_final: 0.6396 (tptp) REVERT: C 899 THR cc_start: 0.8237 (m) cc_final: 0.7870 (p) REVERT: C 1031 GLN cc_start: 0.7736 (mm110) cc_final: 0.7532 (mm110) REVERT: C 1035 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7384 (tttm) REVERT: C 1056 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: C 1084 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7474 (tp-100) REVERT: C 1151 SER cc_start: 0.8617 (m) cc_final: 0.8356 (t) outliers start: 94 outliers final: 35 residues processed: 407 average time/residue: 0.5514 time to fit residues: 269.9899 Evaluate side-chains 369 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET 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 178 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 0.0270 chunk 235 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 240 optimal weight: 0.0050 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN B 812 ASN B 815 GLN B 819 GLN B 832 ASN C 261 GLN C1169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121490 restraints weight = 32951.293| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.33 r_work: 0.3362 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29496 Z= 0.132 Angle : 0.682 21.802 40395 Z= 0.331 Chirality : 0.047 0.426 4848 Planarity : 0.004 0.045 4971 Dihedral : 8.022 65.430 6510 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.99 % Allowed : 13.10 % Favored : 83.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3447 helix: 1.24 (0.20), residues: 702 sheet: 0.04 (0.16), residues: 903 loop : 0.13 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.014 0.001 TYR B 909 PHE 0.020 0.001 PHE C 473 TRP 0.008 0.001 TRP A 960 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00280 (29316) covalent geometry : angle 0.62349 (39906) SS BOND : bond 0.00828 ( 51) SS BOND : angle 3.00987 ( 102) hydrogen bonds : bond 0.04262 ( 1157) hydrogen bonds : angle 5.60545 ( 3024) link_ALPHA1-2 : bond 0.00564 ( 6) link_ALPHA1-2 : angle 1.50485 ( 18) link_ALPHA1-3 : bond 0.01127 ( 15) link_ALPHA1-3 : angle 1.73700 ( 45) link_ALPHA1-6 : bond 0.00894 ( 9) link_ALPHA1-6 : angle 1.58222 ( 27) link_BETA1-4 : bond 0.00911 ( 48) link_BETA1-4 : angle 2.28258 ( 144) link_NAG-ASN : bond 0.00581 ( 51) link_NAG-ASN : angle 2.97296 ( 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 438 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 349 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.5121 (OUTLIER) cc_final: 0.4549 (t0) REVERT: A 542 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7905 (mtt90) REVERT: A 548 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7136 (mt) REVERT: A 600 LEU cc_start: 0.8671 (mt) cc_final: 0.8372 (mm) REVERT: A 614 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7519 (mtt90) REVERT: A 652 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6802 (mmt-90) REVERT: A 666 GLU cc_start: 0.7868 (mp0) cc_final: 0.7531 (mp0) REVERT: A 764 PHE cc_start: 0.8240 (t80) cc_final: 0.7959 (t80) REVERT: A 856 SER cc_start: 0.8723 (t) cc_final: 0.8455 (p) REVERT: A 899 THR cc_start: 0.7992 (m) cc_final: 0.7736 (p) REVERT: A 906 MET cc_start: 0.8313 (ttp) cc_final: 0.8033 (ttm) REVERT: A 913 MET cc_start: 0.5568 (mtt) cc_final: 0.5129 (mmt) REVERT: A 988 GLN cc_start: 0.7748 (tt0) cc_final: 0.7463 (tt0) REVERT: A 995 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7386 (mmmt) REVERT: A 1035 LYS cc_start: 0.7868 (mptt) cc_final: 0.7114 (ttpt) REVERT: A 1068 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7854 (t70) REVERT: A 1151 SER cc_start: 0.8655 (m) cc_final: 0.8392 (t) REVERT: B 141 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7094 (mtp85) REVERT: B 352 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8213 (mm-30) REVERT: B 379 GLU cc_start: 0.7161 (tt0) cc_final: 0.6790 (mm-30) REVERT: B 381 VAL cc_start: 0.8132 (m) cc_final: 0.7869 (p) REVERT: B 536 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: B 764 PHE cc_start: 0.8426 (t80) cc_final: 0.8133 (t80) REVERT: B 777 TYR cc_start: 0.8055 (m-80) cc_final: 0.7451 (m-10) REVERT: B 844 ASP cc_start: 0.6972 (m-30) cc_final: 0.6744 (m-30) REVERT: B 899 THR cc_start: 0.8105 (m) cc_final: 0.7767 (p) REVERT: B 1035 LYS cc_start: 0.7761 (mptt) cc_final: 0.7211 (tttm) REVERT: B 1062 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: B 1105 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: B 1148 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: C 31 ILE cc_start: 0.8075 (mt) cc_final: 0.7786 (mp) REVERT: C 141 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7173 (mtp85) REVERT: C 161 MET cc_start: 0.7829 (mmt) cc_final: 0.7624 (mmp) REVERT: C 381 VAL cc_start: 0.7879 (m) cc_final: 0.7528 (p) REVERT: C 406 ASN cc_start: 0.7734 (m-40) cc_final: 0.7433 (m-40) REVERT: C 536 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6616 (pp20) REVERT: C 614 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7425 (mtt180) REVERT: C 723 PHE cc_start: 0.8065 (m-80) cc_final: 0.7780 (m-80) REVERT: C 777 TYR cc_start: 0.8081 (m-80) cc_final: 0.7650 (m-80) REVERT: C 815 GLN cc_start: 0.7346 (mp10) cc_final: 0.6838 (tp-100) REVERT: C 818 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: C 842 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: C 844 ASP cc_start: 0.7110 (m-30) cc_final: 0.6730 (m-30) REVERT: C 854 LYS cc_start: 0.7129 (tttm) cc_final: 0.6374 (tptp) REVERT: C 899 THR cc_start: 0.8248 (m) cc_final: 0.7934 (p) REVERT: C 995 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7290 (mmmt) REVERT: C 1031 GLN cc_start: 0.7639 (mm110) cc_final: 0.7433 (mm110) REVERT: C 1035 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7365 (tttm) REVERT: C 1056 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: C 1068 ASP cc_start: 0.8043 (t70) cc_final: 0.7502 (m-30) REVERT: C 1084 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7490 (tp-100) REVERT: C 1137 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7921 (mtp) outliers start: 89 outliers final: 41 residues processed: 406 average time/residue: 0.5414 time to fit residues: 264.1893 Evaluate side-chains 386 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET 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 182 optimal weight: 0.3980 chunk 257 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 315 optimal weight: 0.4980 chunk 265 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 278 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 566 GLN A 681 HIS A 812 ASN A 832 ASN B 812 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 812 ASN C1169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120048 restraints weight = 33032.879| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.36 r_work: 0.3349 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29496 Z= 0.147 Angle : 0.717 27.694 40395 Z= 0.344 Chirality : 0.047 0.425 4848 Planarity : 0.004 0.047 4971 Dihedral : 7.604 63.175 6510 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.19 % Allowed : 13.64 % Favored : 83.17 % 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: 0.43 (0.14), residues: 3447 helix: 1.27 (0.20), residues: 702 sheet: 0.08 (0.17), residues: 891 loop : 0.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.018 0.001 TYR C 909 PHE 0.019 0.001 PHE C 473 TRP 0.008 0.001 TRP B 310 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00322 (29316) covalent geometry : angle 0.65149 (39906) SS BOND : bond 0.00900 ( 51) SS BOND : angle 3.08954 ( 102) hydrogen bonds : bond 0.04345 ( 1157) hydrogen bonds : angle 5.53715 ( 3024) link_ALPHA1-2 : bond 0.00552 ( 6) link_ALPHA1-2 : angle 1.49800 ( 18) link_ALPHA1-3 : bond 0.01068 ( 15) link_ALPHA1-3 : angle 1.74147 ( 45) link_ALPHA1-6 : bond 0.00870 ( 9) link_ALPHA1-6 : angle 1.53207 ( 27) link_BETA1-4 : bond 0.00861 ( 48) link_BETA1-4 : angle 2.27393 ( 144) link_NAG-ASN : bond 0.00651 ( 51) link_NAG-ASN : angle 3.49609 ( 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 434 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 339 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6468 (mtmt) REVERT: A 487 ASN cc_start: 0.5077 (OUTLIER) cc_final: 0.4365 (t0) REVERT: A 542 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7917 (mtt90) REVERT: A 600 LEU cc_start: 0.8612 (mt) cc_final: 0.8312 (mm) REVERT: A 614 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7566 (mtt90) REVERT: A 652 ARG cc_start: 0.7356 (mmt90) cc_final: 0.6802 (mmt-90) REVERT: A 666 GLU cc_start: 0.7899 (mp0) cc_final: 0.7585 (mp0) REVERT: A 856 SER cc_start: 0.8730 (t) cc_final: 0.8454 (p) REVERT: A 899 THR cc_start: 0.8006 (m) cc_final: 0.7768 (p) REVERT: A 906 MET cc_start: 0.8344 (ttp) cc_final: 0.8097 (ttm) REVERT: A 913 MET cc_start: 0.5638 (mtt) cc_final: 0.5128 (mmt) REVERT: A 988 GLN cc_start: 0.7826 (tt0) cc_final: 0.7563 (tt0) REVERT: A 995 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7472 (mmmt) REVERT: A 1035 LYS cc_start: 0.7834 (mptt) cc_final: 0.7135 (ttpt) REVERT: A 1068 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7866 (t70) REVERT: A 1148 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 1151 SER cc_start: 0.8696 (m) cc_final: 0.8419 (t) REVERT: B 141 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7114 (mtp85) REVERT: B 369 LYS cc_start: 0.6381 (mptt) cc_final: 0.6086 (mptp) REVERT: B 379 GLU cc_start: 0.7213 (tt0) cc_final: 0.6781 (mm-30) REVERT: B 381 VAL cc_start: 0.8207 (m) cc_final: 0.7920 (p) REVERT: B 487 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6034 (t0) REVERT: B 536 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: B 600 LEU cc_start: 0.8508 (mt) cc_final: 0.8173 (mm) REVERT: B 764 PHE cc_start: 0.8450 (t80) cc_final: 0.8153 (t80) REVERT: B 777 TYR cc_start: 0.8082 (m-80) cc_final: 0.7460 (m-10) REVERT: B 844 ASP cc_start: 0.6957 (m-30) cc_final: 0.6743 (m-30) REVERT: B 899 THR cc_start: 0.8135 (m) cc_final: 0.7796 (p) REVERT: B 1062 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: B 1105 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: B 1148 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: C 31 ILE cc_start: 0.8106 (mt) cc_final: 0.7803 (mp) REVERT: C 93 THR cc_start: 0.8104 (p) cc_final: 0.7803 (t) REVERT: C 141 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7188 (mtp85) REVERT: C 252 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: C 381 VAL cc_start: 0.7864 (m) cc_final: 0.7512 (p) REVERT: C 406 ASN cc_start: 0.7811 (m-40) cc_final: 0.7515 (m-40) REVERT: C 536 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: C 612 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8339 (m) REVERT: C 614 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7588 (mtt180) REVERT: C 777 TYR cc_start: 0.8115 (m-80) cc_final: 0.7677 (m-80) REVERT: C 815 GLN cc_start: 0.7297 (mp10) cc_final: 0.6755 (tp-100) REVERT: C 818 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: C 842 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: C 844 ASP cc_start: 0.7187 (m-30) cc_final: 0.6767 (m-30) REVERT: C 854 LYS cc_start: 0.7137 (tttm) cc_final: 0.6336 (tptp) REVERT: C 899 THR cc_start: 0.8297 (m) cc_final: 0.8017 (p) REVERT: C 995 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7355 (mmmt) REVERT: C 1031 GLN cc_start: 0.7691 (mm110) cc_final: 0.7457 (mm110) REVERT: C 1035 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7407 (tttm) REVERT: C 1056 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: C 1068 ASP cc_start: 0.8152 (t70) cc_final: 0.7555 (m-30) REVERT: C 1084 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7507 (tp-100) outliers start: 95 outliers final: 48 residues processed: 399 average time/residue: 0.5581 time to fit residues: 266.7697 Evaluate side-chains 394 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1157 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 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 114 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A 681 HIS A1009 GLN B 427 GLN B 812 ASN B 832 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 427 GLN C 812 ASN C1169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118573 restraints weight = 33035.096| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.35 r_work: 0.3329 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 29496 Z= 0.183 Angle : 0.739 27.844 40395 Z= 0.359 Chirality : 0.048 0.410 4848 Planarity : 0.004 0.051 4971 Dihedral : 7.538 62.584 6510 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.39 % Allowed : 13.61 % Favored : 83.00 % 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: 0.30 (0.14), residues: 3447 helix: 1.12 (0.20), residues: 705 sheet: 0.06 (0.16), residues: 921 loop : 0.03 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.011 0.001 TYR B1141 PHE 0.022 0.002 PHE C 473 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00417 (29316) covalent geometry : angle 0.67549 (39906) SS BOND : bond 0.00945 ( 51) SS BOND : angle 3.55171 ( 102) hydrogen bonds : bond 0.04616 ( 1157) hydrogen bonds : angle 5.63396 ( 3024) link_ALPHA1-2 : bond 0.00580 ( 6) link_ALPHA1-2 : angle 1.47797 ( 18) link_ALPHA1-3 : bond 0.01007 ( 15) link_ALPHA1-3 : angle 1.71682 ( 45) link_ALPHA1-6 : bond 0.00805 ( 9) link_ALPHA1-6 : angle 1.58154 ( 27) link_BETA1-4 : bond 0.00803 ( 48) link_BETA1-4 : angle 2.24052 ( 144) link_NAG-ASN : bond 0.00560 ( 51) link_NAG-ASN : angle 3.24705 ( 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 428 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 327 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6944 (mtpp) cc_final: 0.6499 (mtmt) REVERT: A 473 PHE cc_start: 0.7990 (m-80) cc_final: 0.7696 (m-80) REVERT: A 487 ASN cc_start: 0.5037 (OUTLIER) cc_final: 0.4364 (t0) REVERT: A 542 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7937 (mtt90) REVERT: A 600 LEU cc_start: 0.8617 (mt) cc_final: 0.8304 (mm) REVERT: A 614 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7530 (mtt90) REVERT: A 652 ARG cc_start: 0.7364 (mmt90) cc_final: 0.6825 (mmt-90) REVERT: A 666 GLU cc_start: 0.7842 (mp0) cc_final: 0.7567 (mp0) REVERT: A 856 SER cc_start: 0.8738 (t) cc_final: 0.8454 (p) REVERT: A 899 THR cc_start: 0.8013 (m) cc_final: 0.7792 (p) REVERT: A 906 MET cc_start: 0.8357 (ttp) cc_final: 0.8059 (ttm) REVERT: A 913 MET cc_start: 0.5690 (mtt) cc_final: 0.5126 (mmt) REVERT: A 988 GLN cc_start: 0.7755 (tt0) cc_final: 0.7471 (tt0) REVERT: A 995 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7507 (mmmt) REVERT: A 1035 LYS cc_start: 0.7863 (mptt) cc_final: 0.7157 (ttpt) REVERT: A 1068 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7860 (t70) REVERT: A 1151 SER cc_start: 0.8744 (m) cc_final: 0.8421 (t) REVERT: B 141 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7043 (mtp180) REVERT: B 252 GLU cc_start: 0.7846 (pt0) cc_final: 0.7292 (pt0) REVERT: B 319 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: B 369 LYS cc_start: 0.6501 (mptt) cc_final: 0.6171 (mptp) REVERT: B 379 GLU cc_start: 0.7309 (tt0) cc_final: 0.6827 (mm-30) REVERT: B 381 VAL cc_start: 0.8203 (m) cc_final: 0.7922 (p) REVERT: B 487 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6380 (t0) REVERT: B 488 LEU cc_start: 0.6627 (tp) cc_final: 0.6370 (tt) REVERT: B 509 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.6026 (p0) REVERT: B 536 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: B 587 LYS cc_start: 0.7839 (mptt) cc_final: 0.7593 (mptp) REVERT: B 600 LEU cc_start: 0.8527 (mt) cc_final: 0.8170 (mm) REVERT: B 777 TYR cc_start: 0.8194 (m-80) cc_final: 0.7547 (m-10) REVERT: B 899 THR cc_start: 0.8284 (m) cc_final: 0.7886 (p) REVERT: B 1062 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: B 1105 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: C 31 ILE cc_start: 0.8124 (mt) cc_final: 0.7826 (mp) REVERT: C 93 THR cc_start: 0.7868 (p) cc_final: 0.7540 (t) REVERT: C 141 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7184 (mtp85) REVERT: C 188 GLU cc_start: 0.8358 (tt0) cc_final: 0.8149 (mt-10) REVERT: C 252 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: C 303 ILE cc_start: 0.8091 (pt) cc_final: 0.7742 (pp) REVERT: C 406 ASN cc_start: 0.7837 (m-40) cc_final: 0.7543 (m-40) REVERT: C 536 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6615 (pp20) REVERT: C 566 GLN cc_start: 0.8220 (mt0) cc_final: 0.7958 (mt0) REVERT: C 612 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 614 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7638 (mtt180) REVERT: C 777 TYR cc_start: 0.8197 (m-80) cc_final: 0.7786 (m-80) REVERT: C 812 ASN cc_start: 0.8802 (t0) cc_final: 0.8236 (t160) REVERT: C 815 GLN cc_start: 0.7313 (mp10) cc_final: 0.6775 (tp-100) REVERT: C 818 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: C 842 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: C 844 ASP cc_start: 0.7278 (m-30) cc_final: 0.6834 (m-30) REVERT: C 899 THR cc_start: 0.8279 (m) cc_final: 0.8014 (p) REVERT: C 995 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7394 (mmmt) REVERT: C 1031 GLN cc_start: 0.7658 (mm110) cc_final: 0.7423 (mm110) REVERT: C 1035 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7438 (tttm) REVERT: C 1056 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: C 1068 ASP cc_start: 0.8146 (t70) cc_final: 0.7556 (m-30) REVERT: C 1084 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (tp-100) outliers start: 101 outliers final: 53 residues processed: 393 average time/residue: 0.5227 time to fit residues: 247.6590 Evaluate side-chains 383 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU 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 255 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 566 GLN B 812 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 733 GLN C1009 GLN C1169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119433 restraints weight = 33103.578| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.36 r_work: 0.3339 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 29496 Z= 0.162 Angle : 0.720 26.571 40395 Z= 0.351 Chirality : 0.048 0.414 4848 Planarity : 0.004 0.051 4971 Dihedral : 7.345 61.336 6510 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.96 % Allowed : 14.08 % Favored : 82.96 % 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: 0.28 (0.14), residues: 3447 helix: 1.13 (0.20), residues: 705 sheet: 0.08 (0.16), residues: 906 loop : -0.03 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.017 0.001 TYR B 909 PHE 0.021 0.002 PHE C 473 TRP 0.009 0.001 TRP B 310 HIS 0.003 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00367 (29316) covalent geometry : angle 0.65566 (39906) SS BOND : bond 0.01038 ( 51) SS BOND : angle 3.69195 ( 102) hydrogen bonds : bond 0.04466 ( 1157) hydrogen bonds : angle 5.68410 ( 3024) link_ALPHA1-2 : bond 0.00564 ( 6) link_ALPHA1-2 : angle 1.48548 ( 18) link_ALPHA1-3 : bond 0.00989 ( 15) link_ALPHA1-3 : angle 1.68048 ( 45) link_ALPHA1-6 : bond 0.00825 ( 9) link_ALPHA1-6 : angle 1.53423 ( 27) link_BETA1-4 : bond 0.00794 ( 48) link_BETA1-4 : angle 2.16840 ( 144) link_NAG-ASN : bond 0.00552 ( 51) link_NAG-ASN : angle 3.14052 ( 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 408 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 320 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.7091 (mtpp) cc_final: 0.6608 (mtmt) REVERT: A 473 PHE cc_start: 0.7957 (m-80) cc_final: 0.7627 (m-80) REVERT: A 487 ASN cc_start: 0.4950 (OUTLIER) cc_final: 0.4181 (t0) REVERT: A 542 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7933 (mtt90) REVERT: A 600 LEU cc_start: 0.8620 (mt) cc_final: 0.8294 (mm) REVERT: A 614 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7533 (mtt90) REVERT: A 652 ARG cc_start: 0.7315 (mmt90) cc_final: 0.6792 (mmt-90) REVERT: A 666 GLU cc_start: 0.7889 (mp0) cc_final: 0.7623 (mp0) REVERT: A 832 ASN cc_start: 0.8617 (m110) cc_final: 0.8296 (m-40) REVERT: A 856 SER cc_start: 0.8735 (t) cc_final: 0.8444 (p) REVERT: A 899 THR cc_start: 0.8047 (m) cc_final: 0.7821 (p) REVERT: A 906 MET cc_start: 0.8354 (ttp) cc_final: 0.8064 (ttm) REVERT: A 913 MET cc_start: 0.5628 (mtt) cc_final: 0.5097 (mmt) REVERT: A 988 GLN cc_start: 0.7701 (tt0) cc_final: 0.7426 (tt0) REVERT: A 995 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7496 (mmmt) REVERT: A 1035 LYS cc_start: 0.7840 (mptt) cc_final: 0.7154 (ttpt) REVERT: A 1068 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7863 (t70) REVERT: A 1151 SER cc_start: 0.8713 (m) cc_final: 0.8415 (t) REVERT: B 141 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7050 (mtp180) REVERT: B 252 GLU cc_start: 0.7842 (pt0) cc_final: 0.7283 (pt0) REVERT: B 319 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: B 369 LYS cc_start: 0.6634 (mptt) cc_final: 0.6315 (mptp) REVERT: B 379 GLU cc_start: 0.7344 (tt0) cc_final: 0.6837 (mm-30) REVERT: B 381 VAL cc_start: 0.8191 (m) cc_final: 0.7906 (p) REVERT: B 427 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: B 487 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6550 (t0) REVERT: B 488 LEU cc_start: 0.6533 (tp) cc_final: 0.6295 (tt) REVERT: B 509 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.6037 (p0) REVERT: B 536 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6900 (pp20) REVERT: B 587 LYS cc_start: 0.7802 (mptt) cc_final: 0.7575 (mptp) REVERT: B 600 LEU cc_start: 0.8503 (mt) cc_final: 0.8138 (mm) REVERT: B 764 PHE cc_start: 0.8323 (t80) cc_final: 0.7876 (t80) REVERT: B 777 TYR cc_start: 0.8188 (m-80) cc_final: 0.7530 (m-10) REVERT: B 899 THR cc_start: 0.8241 (m) cc_final: 0.7858 (p) REVERT: B 1062 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: B 1105 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: C 31 ILE cc_start: 0.8095 (mt) cc_final: 0.7788 (mp) REVERT: C 93 THR cc_start: 0.7805 (p) cc_final: 0.7463 (t) REVERT: C 141 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7190 (mtp85) REVERT: C 161 MET cc_start: 0.7965 (mmp) cc_final: 0.7585 (mmm) REVERT: C 252 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: C 303 ILE cc_start: 0.8062 (pt) cc_final: 0.7709 (pp) REVERT: C 406 ASN cc_start: 0.7821 (m-40) cc_final: 0.7498 (m-40) REVERT: C 536 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: C 548 LEU cc_start: 0.7146 (mp) cc_final: 0.6756 (tp) REVERT: C 612 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8272 (m) REVERT: C 614 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7607 (mtt180) REVERT: C 777 TYR cc_start: 0.8182 (m-80) cc_final: 0.7763 (m-80) REVERT: C 812 ASN cc_start: 0.8782 (t0) cc_final: 0.8227 (t160) REVERT: C 815 GLN cc_start: 0.7332 (mp10) cc_final: 0.6785 (tp-100) REVERT: C 818 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: C 842 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: C 844 ASP cc_start: 0.7299 (m-30) cc_final: 0.6856 (m-30) REVERT: C 899 THR cc_start: 0.8231 (m) cc_final: 0.7983 (p) REVERT: C 995 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7412 (mmmt) REVERT: C 1031 GLN cc_start: 0.7634 (mm110) cc_final: 0.7401 (mm110) REVERT: C 1035 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7432 (tttm) REVERT: C 1056 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: C 1068 ASP cc_start: 0.8165 (t70) cc_final: 0.7570 (m-30) REVERT: C 1084 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (tp-100) outliers start: 88 outliers final: 53 residues processed: 375 average time/residue: 0.5463 time to fit residues: 246.5719 Evaluate side-chains 378 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 309 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR 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 100 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 309 optimal weight: 0.5980 chunk 239 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 812 ASN B 832 ASN B1009 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 815 GLN C1009 GLN C1169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118917 restraints weight = 33020.383| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.36 r_work: 0.3333 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 29496 Z= 0.174 Angle : 0.733 27.518 40395 Z= 0.358 Chirality : 0.048 0.396 4848 Planarity : 0.004 0.052 4971 Dihedral : 7.260 60.744 6510 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.02 % Allowed : 14.08 % Favored : 82.90 % 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: 0.22 (0.14), residues: 3447 helix: 1.10 (0.20), residues: 705 sheet: 0.05 (0.17), residues: 891 loop : -0.08 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.014 0.001 TYR B 909 PHE 0.022 0.002 PHE C 473 TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00398 (29316) covalent geometry : angle 0.67292 (39906) SS BOND : bond 0.01001 ( 51) SS BOND : angle 3.62342 ( 102) hydrogen bonds : bond 0.04563 ( 1157) hydrogen bonds : angle 5.69473 ( 3024) link_ALPHA1-2 : bond 0.00566 ( 6) link_ALPHA1-2 : angle 1.47934 ( 18) link_ALPHA1-3 : bond 0.00946 ( 15) link_ALPHA1-3 : angle 1.67604 ( 45) link_ALPHA1-6 : bond 0.00786 ( 9) link_ALPHA1-6 : angle 1.55391 ( 27) link_BETA1-4 : bond 0.00764 ( 48) link_BETA1-4 : angle 2.15823 ( 144) link_NAG-ASN : bond 0.00521 ( 51) link_NAG-ASN : angle 3.03471 ( 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 404 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 314 time to evaluate : 0.978 Fit side-chains REVERT: A 52 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6547 (mttt) REVERT: A 473 PHE cc_start: 0.8025 (m-80) cc_final: 0.7711 (m-80) REVERT: A 487 ASN cc_start: 0.5195 (OUTLIER) cc_final: 0.4418 (t0) REVERT: A 542 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7931 (mtt90) REVERT: A 600 LEU cc_start: 0.8628 (mt) cc_final: 0.8305 (mm) REVERT: A 614 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7594 (mtt90) REVERT: A 652 ARG cc_start: 0.7350 (mmt90) cc_final: 0.6811 (mmt-90) REVERT: A 666 GLU cc_start: 0.7864 (mp0) cc_final: 0.7598 (mp0) REVERT: A 832 ASN cc_start: 0.8509 (m110) cc_final: 0.8146 (m-40) REVERT: A 856 SER cc_start: 0.8734 (t) cc_final: 0.8440 (p) REVERT: A 899 THR cc_start: 0.8053 (m) cc_final: 0.7845 (p) REVERT: A 906 MET cc_start: 0.8342 (ttp) cc_final: 0.8041 (ttm) REVERT: A 913 MET cc_start: 0.5649 (mtt) cc_final: 0.5111 (mmt) REVERT: A 988 GLN cc_start: 0.7705 (tt0) cc_final: 0.7436 (tt0) REVERT: A 995 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7537 (mmmt) REVERT: A 1035 LYS cc_start: 0.7853 (mptt) cc_final: 0.7174 (ttpt) REVERT: A 1068 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7869 (t70) REVERT: A 1151 SER cc_start: 0.8713 (m) cc_final: 0.8402 (t) REVERT: B 141 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7046 (mtp180) REVERT: B 252 GLU cc_start: 0.7825 (pt0) cc_final: 0.7265 (pt0) REVERT: B 319 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: B 369 LYS cc_start: 0.6671 (mptt) cc_final: 0.6365 (mptp) REVERT: B 379 GLU cc_start: 0.7310 (tt0) cc_final: 0.6807 (mm-30) REVERT: B 381 VAL cc_start: 0.8077 (m) cc_final: 0.7775 (p) REVERT: B 427 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: B 487 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6639 (t0) REVERT: B 488 LEU cc_start: 0.6580 (tp) cc_final: 0.6324 (tt) REVERT: B 509 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5868 (p0) REVERT: B 536 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: B 587 LYS cc_start: 0.7802 (mptt) cc_final: 0.7589 (mptp) REVERT: B 600 LEU cc_start: 0.8503 (mt) cc_final: 0.8136 (mm) REVERT: B 764 PHE cc_start: 0.8381 (t80) cc_final: 0.7983 (t80) REVERT: B 812 ASN cc_start: 0.8809 (t0) cc_final: 0.8281 (t160) REVERT: B 899 THR cc_start: 0.8228 (m) cc_final: 0.7864 (p) REVERT: B 1062 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: B 1105 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 31 ILE cc_start: 0.8085 (mt) cc_final: 0.7789 (mp) REVERT: C 141 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7188 (mtp85) REVERT: C 161 MET cc_start: 0.7890 (mmp) cc_final: 0.7517 (mmm) REVERT: C 252 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: C 303 ILE cc_start: 0.8069 (pt) cc_final: 0.7722 (pp) REVERT: C 406 ASN cc_start: 0.7830 (m-40) cc_final: 0.7508 (m-40) REVERT: C 536 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: C 548 LEU cc_start: 0.7097 (mp) cc_final: 0.6832 (tp) REVERT: C 566 GLN cc_start: 0.8227 (mt0) cc_final: 0.8013 (mt0) REVERT: C 612 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 614 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7621 (mtt180) REVERT: C 777 TYR cc_start: 0.8209 (m-80) cc_final: 0.7784 (m-80) REVERT: C 815 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6882 (tp-100) REVERT: C 818 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: C 842 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: C 844 ASP cc_start: 0.7296 (m-30) cc_final: 0.6852 (m-30) REVERT: C 899 THR cc_start: 0.8228 (m) cc_final: 0.8010 (p) REVERT: C 995 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7441 (mmmt) REVERT: C 1031 GLN cc_start: 0.7647 (mm110) cc_final: 0.7413 (mm110) REVERT: C 1035 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7445 (tttm) REVERT: C 1056 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: C 1068 ASP cc_start: 0.8163 (t70) cc_final: 0.7571 (m-30) REVERT: C 1084 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7653 (tp-100) outliers start: 90 outliers final: 55 residues processed: 369 average time/residue: 0.5570 time to fit residues: 246.8931 Evaluate side-chains 381 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR 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 200 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 209 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A1009 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 815 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119957 restraints weight = 32934.244| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.35 r_work: 0.3346 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 29496 Z= 0.149 Angle : 0.723 27.303 40395 Z= 0.353 Chirality : 0.047 0.382 4848 Planarity : 0.004 0.052 4971 Dihedral : 7.127 59.788 6510 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.76 % Allowed : 14.52 % Favored : 82.73 % 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: 0.25 (0.14), residues: 3447 helix: 1.15 (0.20), residues: 705 sheet: 0.07 (0.17), residues: 888 loop : -0.07 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 542 TYR 0.021 0.001 TYR B 777 PHE 0.024 0.001 PHE B 571 TRP 0.009 0.001 TRP B 310 HIS 0.003 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00331 (29316) covalent geometry : angle 0.65968 (39906) SS BOND : bond 0.00950 ( 51) SS BOND : angle 3.73855 ( 102) hydrogen bonds : bond 0.04374 ( 1157) hydrogen bonds : angle 5.69359 ( 3024) link_ALPHA1-2 : bond 0.00561 ( 6) link_ALPHA1-2 : angle 1.48318 ( 18) link_ALPHA1-3 : bond 0.00933 ( 15) link_ALPHA1-3 : angle 1.66187 ( 45) link_ALPHA1-6 : bond 0.00813 ( 9) link_ALPHA1-6 : angle 1.50542 ( 27) link_BETA1-4 : bond 0.00765 ( 48) link_BETA1-4 : angle 2.09535 ( 144) link_NAG-ASN : bond 0.00576 ( 51) link_NAG-ASN : angle 3.10161 ( 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 395 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 313 time to evaluate : 0.996 Fit side-chains REVERT: A 52 LYS cc_start: 0.7071 (mtpp) cc_final: 0.6603 (mttt) REVERT: A 473 PHE cc_start: 0.7963 (m-80) cc_final: 0.7634 (m-80) REVERT: A 487 ASN cc_start: 0.5011 (OUTLIER) cc_final: 0.4152 (t0) REVERT: A 600 LEU cc_start: 0.8612 (mt) cc_final: 0.8281 (mm) REVERT: A 614 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7574 (mtt90) REVERT: A 652 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6828 (mmt-90) REVERT: A 666 GLU cc_start: 0.7887 (mp0) cc_final: 0.7616 (mp0) REVERT: A 832 ASN cc_start: 0.8444 (m110) cc_final: 0.8074 (m-40) REVERT: A 856 SER cc_start: 0.8730 (t) cc_final: 0.8438 (p) REVERT: A 899 THR cc_start: 0.8049 (m) cc_final: 0.7843 (p) REVERT: A 906 MET cc_start: 0.8323 (ttp) cc_final: 0.8027 (ttm) REVERT: A 913 MET cc_start: 0.5610 (mtt) cc_final: 0.5076 (mmt) REVERT: A 988 GLN cc_start: 0.7710 (tt0) cc_final: 0.7446 (tt0) REVERT: A 995 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7523 (mmmt) REVERT: A 1035 LYS cc_start: 0.7829 (mptt) cc_final: 0.7159 (ttpt) REVERT: A 1068 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7847 (t70) REVERT: A 1151 SER cc_start: 0.8686 (m) cc_final: 0.8410 (t) REVERT: B 141 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7048 (mtp180) REVERT: B 252 GLU cc_start: 0.7802 (pt0) cc_final: 0.7242 (pt0) REVERT: B 319 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: B 369 LYS cc_start: 0.6635 (mptt) cc_final: 0.6346 (mptp) REVERT: B 379 GLU cc_start: 0.7369 (tt0) cc_final: 0.6815 (mm-30) REVERT: B 381 VAL cc_start: 0.8052 (m) cc_final: 0.7755 (p) REVERT: B 427 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: B 487 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6725 (t0) REVERT: B 509 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5955 (p0) REVERT: B 536 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6914 (pp20) REVERT: B 587 LYS cc_start: 0.7810 (mptt) cc_final: 0.7598 (mptp) REVERT: B 600 LEU cc_start: 0.8486 (mt) cc_final: 0.8111 (mm) REVERT: B 764 PHE cc_start: 0.8442 (t80) cc_final: 0.7950 (t80) REVERT: B 777 TYR cc_start: 0.7899 (m-80) cc_final: 0.7526 (m-10) REVERT: B 812 ASN cc_start: 0.8797 (t0) cc_final: 0.8312 (t160) REVERT: B 899 THR cc_start: 0.8190 (m) cc_final: 0.7822 (p) REVERT: B 1062 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: B 1105 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: C 31 ILE cc_start: 0.8065 (mt) cc_final: 0.7763 (mp) REVERT: C 141 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7182 (mtp85) REVERT: C 161 MET cc_start: 0.7975 (mmp) cc_final: 0.7667 (mmm) REVERT: C 252 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: C 303 ILE cc_start: 0.8061 (pt) cc_final: 0.7710 (pp) REVERT: C 406 ASN cc_start: 0.7811 (m-40) cc_final: 0.7490 (m-40) REVERT: C 536 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6631 (pp20) REVERT: C 548 LEU cc_start: 0.7039 (mp) cc_final: 0.6787 (tp) REVERT: C 566 GLN cc_start: 0.8209 (mt0) cc_final: 0.7994 (mt0) REVERT: C 612 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8271 (m) REVERT: C 614 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7606 (mtt180) REVERT: C 765 ASN cc_start: 0.7994 (t0) cc_final: 0.7329 (m-40) REVERT: C 777 TYR cc_start: 0.8173 (m-80) cc_final: 0.7789 (m-80) REVERT: C 818 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: C 842 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: C 844 ASP cc_start: 0.7286 (m-30) cc_final: 0.6844 (m-30) REVERT: C 995 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7430 (mmmt) REVERT: C 1031 GLN cc_start: 0.7620 (mm110) cc_final: 0.7389 (mm110) REVERT: C 1035 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7429 (tttm) REVERT: C 1056 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: C 1068 ASP cc_start: 0.8164 (t70) cc_final: 0.7564 (m-30) REVERT: C 1084 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7666 (tp-100) outliers start: 82 outliers final: 55 residues processed: 364 average time/residue: 0.5549 time to fit residues: 242.9817 Evaluate side-chains 377 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 306 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR 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 289 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 340 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 576 GLN B 733 GLN B 832 ASN B1009 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C1009 GLN C1169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119006 restraints weight = 33196.775| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.34 r_work: 0.3336 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 29496 Z= 0.173 Angle : 0.733 27.586 40395 Z= 0.358 Chirality : 0.048 0.380 4848 Planarity : 0.004 0.051 4971 Dihedral : 7.107 59.368 6510 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.82 % Allowed : 14.65 % Favored : 82.53 % 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: 0.19 (0.14), residues: 3447 helix: 1.10 (0.20), residues: 705 sheet: 0.02 (0.16), residues: 921 loop : -0.10 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 542 TYR 0.019 0.001 TYR B 777 PHE 0.024 0.002 PHE B 571 TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00393 (29316) covalent geometry : angle 0.67258 (39906) SS BOND : bond 0.00994 ( 51) SS BOND : angle 3.69720 ( 102) hydrogen bonds : bond 0.04534 ( 1157) hydrogen bonds : angle 5.71002 ( 3024) link_ALPHA1-2 : bond 0.00565 ( 6) link_ALPHA1-2 : angle 1.48252 ( 18) link_ALPHA1-3 : bond 0.00898 ( 15) link_ALPHA1-3 : angle 1.67226 ( 45) link_ALPHA1-6 : bond 0.00766 ( 9) link_ALPHA1-6 : angle 1.54310 ( 27) link_BETA1-4 : bond 0.00743 ( 48) link_BETA1-4 : angle 2.09490 ( 144) link_NAG-ASN : bond 0.00527 ( 51) link_NAG-ASN : angle 3.02553 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11205.80 seconds wall clock time: 191 minutes 20.40 seconds (11480.40 seconds total)