Starting phenix.real_space_refine on Thu Sep 18 13:54:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3d_46532/09_2025/9d3d_46532.map" } resolution = 3.41 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= 0.001 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 119 5.16 5 C 10719 2.51 5 N 2819 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17243 Number of models: 1 Model: "" Number of chains: 50 Chain: "C" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3543 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "c" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "a" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1007 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "b" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "l" 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: "m" 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: "n" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7, 'PO4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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 Time building chain proxies: 4.37, per 1000 atoms: 0.25 Number of scatterers: 17243 At special positions: 0 Unit cell: (128.65, 124.5, 167.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 1 15.00 O 3585 8.00 N 2819 7.00 C 10719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS a 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS b 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS a 598 " - pdb=" SG CYS a 604 " distance=2.03 Simple disulfide: pdb=" SG CYS b 598 " - pdb=" SG CYS b 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 P 4 " - " MAN P 5 " " MAN R 4 " - " MAN R 5 " " MAN p 4 " - " MAN p 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA h 3 " - " MAN h 4 " " BMA l 3 " - " MAN l 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " " BMA h 3 " - " MAN h 5 " " BMA p 3 " - " MAN p 6 " " BMA r 3 " - " MAN r 6 " BETA1-3 " NAG m 2 " - " BMA m 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " 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 l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " 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-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 137 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 234 " " NAG B 603 " - " ASN B 301 " " NAG B 604 " - " ASN B 339 " " NAG B 605 " - " ASN B 355 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 137 " " NAG D 1 " - " ASN C 295 " " NAG E 1 " - " ASN C 386 " " NAG F 1 " - " ASN C 363 " " NAG G 1 " - " ASN C 160 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 392 " " NAG K 1 " - " ASN C 301 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 448 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN A 392 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 332 " " NAG a 701 " - " ASN a 611 " " NAG a 702 " - " ASN a 637 " " NAG b 701 " - " ASN b 611 " " NAG b 702 " - " ASN b 637 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG d 1 " - " ASN B 332 " " NAG e 1 " - " ASN B 386 " " NAG f 1 " - " ASN B 363 " " NAG g 1 " - " ASN B 197 " " NAG h 1 " - " ASN B 160 " " NAG i 1 " - " ASN B 295 " " NAG j 1 " - " ASN B 133 " " NAG k 1 " - " ASN B 137 " " NAG l 1 " - " ASN B 156 " " NAG m 1 " - " ASN B 276 " " NAG n 1 " - " ASN B 392 " " NAG o 1 " - " ASN B 448 " " NAG p 1 " - " ASN C 262 " " NAG q 1 " - " ASN C 276 " " NAG r 1 " - " ASN B 262 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 729.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 23.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.531A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.623A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.510A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.998A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.979A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.630A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.650A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.722A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.608A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.462A pdb=" N GLY A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.065A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.289A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.328A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.608A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 542 Processing helix chain 'c' and resid 572 through 596 removed outlier: 4.048A pdb=" N LEU c 576 " --> pdb=" O GLY c 572 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL c 583 " --> pdb=" O ARG c 579 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 615 Processing helix chain 'c' and resid 627 through 633 Processing helix chain 'c' and resid 634 through 635 No H-bonds generated for 'chain 'c' and resid 634 through 635' Processing helix chain 'c' and resid 636 through 637 No H-bonds generated for 'chain 'c' and resid 636 through 637' Processing helix chain 'c' and resid 638 through 664 removed outlier: 4.048A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN c 651 " --> pdb=" O GLU c 647 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN c 653 " --> pdb=" O SER c 649 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA c 662 " --> pdb=" O GLN c 658 " (cutoff:3.500A) Processing helix chain 'a' and resid 529 through 534 Processing helix chain 'a' and resid 536 through 542 removed outlier: 4.411A pdb=" N GLN a 540 " --> pdb=" O THR a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 569 through 571 No H-bonds generated for 'chain 'a' and resid 569 through 571' Processing helix chain 'a' and resid 572 through 595 removed outlier: 3.618A pdb=" N ARG a 588 " --> pdb=" O GLU a 584 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 627 through 635 removed outlier: 4.201A pdb=" N LYS a 633 " --> pdb=" O LEU a 629 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU a 634 " --> pdb=" O GLN a 630 " (cutoff:3.500A) Processing helix chain 'a' and resid 638 through 663 removed outlier: 3.693A pdb=" N GLY a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU a 647 " --> pdb=" O TYR a 643 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN a 652 " --> pdb=" O GLU a 648 " (cutoff:3.500A) Processing helix chain 'b' and resid 529 through 534 Processing helix chain 'b' and resid 536 through 542 removed outlier: 4.166A pdb=" N GLN b 540 " --> pdb=" O THR b 536 " (cutoff:3.500A) Processing helix chain 'b' and resid 570 through 596 removed outlier: 3.838A pdb=" N LYS b 574 " --> pdb=" O VAL b 570 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 576 " --> pdb=" O GLY b 572 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA b 578 " --> pdb=" O LYS b 574 " (cutoff:3.500A) Processing helix chain 'b' and resid 618 through 625 removed outlier: 3.839A pdb=" N ILE b 622 " --> pdb=" O ASN b 618 " (cutoff:3.500A) Processing helix chain 'b' and resid 627 through 636 removed outlier: 4.072A pdb=" N LYS b 633 " --> pdb=" O LEU b 629 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU b 634 " --> pdb=" O GLN b 630 " (cutoff:3.500A) Processing helix chain 'b' and resid 638 through 661 removed outlier: 3.515A pdb=" N GLU b 647 " --> pdb=" O TYR b 643 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU b 648 " --> pdb=" O GLY b 644 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN b 653 " --> pdb=" O SER b 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 5.798A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.388A pdb=" N VAL C 36 " --> pdb=" O THR c 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.061A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.030A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.575A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.253A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.190A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.586A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.190A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 421 removed outlier: 3.576A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.756A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.537A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL A 36 " --> pdb=" O THR a 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.758A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.728A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.642A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AB6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.507A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.804A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 413 through 418 removed outlier: 4.152A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AC3, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.687A pdb=" N VAL b 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL B 38 " --> pdb=" O THR b 606 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR b 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR B 40 " --> pdb=" O CYS b 604 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N CYS b 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.863A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.888A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.735A pdb=" N VAL B 120 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'B' and resid 271 through 273 removed outlier: 12.276A pdb=" N ILE B 284 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ASP B 457 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.233A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 457 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.700A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.700A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.574A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.650A pdb=" N CYS H 92 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP H 108 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR H 94 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS H 98 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU H 102 " --> pdb=" O HIS H 98 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU H 100 " --> pdb=" O ASP H 100R" (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP H 100R" --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP H 100B" --> pdb=" O TRP H 100P" (cutoff:3.500A) removed outlier: 7.239A pdb=" N TRP H 100P" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE H 100D" --> pdb=" O GLU H 100N" (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU H 100N" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.935A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.401A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG L 39 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS L 49 " --> pdb=" O HIS L 53 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1491 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: 3.25 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5205 1.34 - 1.46: 4032 1.46 - 1.58: 8170 1.58 - 1.70: 2 1.70 - 1.82: 157 Bond restraints: 17566 Sorted by residual: bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.510 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" O3 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.458 1.509 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" O2 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.461 1.510 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.462 1.510 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.462 1.508 -0.046 2.00e-02 2.50e+03 5.33e+00 ... (remaining 17561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 23700 2.71 - 5.42: 141 5.42 - 8.12: 3 8.12 - 10.83: 3 10.83 - 13.54: 2 Bond angle restraints: 23849 Sorted by residual: angle pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" pdb=" O2 TYS H 100F" ideal model delta sigma weight residual 114.11 100.57 13.54 3.00e+00 1.11e-01 2.04e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O2 TYS H 100I" ideal model delta sigma weight residual 114.11 101.23 12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" OH TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 100.21 110.32 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OH TYS H 100F" pdb=" S TYS H 100F" pdb=" O3 TYS H 100F" ideal model delta sigma weight residual 100.21 109.58 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" OH TYS H 100F" pdb=" S TYS H 100F" pdb=" O2 TYS H 100F" ideal model delta sigma weight residual 104.74 114.11 -9.37 3.00e+00 1.11e-01 9.75e+00 ... (remaining 23844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 11489 16.66 - 33.32: 504 33.32 - 49.98: 151 49.98 - 66.64: 46 66.64 - 83.30: 6 Dihedral angle restraints: 12196 sinusoidal: 6513 harmonic: 5683 Sorted by residual: dihedral pdb=" CA ASN A 448 " pdb=" C ASN A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.44 32.44 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -117.28 31.28 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 12193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2748 0.068 - 0.136: 294 0.136 - 0.203: 15 0.203 - 0.271: 3 0.271 - 0.339: 1 Chirality restraints: 3061 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG B 605 " pdb=" ND2 ASN B 355 " pdb=" C2 NAG B 605 " pdb=" O5 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3058 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO B 212 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO C 43 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 298 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 299 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.017 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 131 2.56 - 3.14: 14312 3.14 - 3.73: 23788 3.73 - 4.31: 35302 4.31 - 4.90: 59742 Nonbonded interactions: 133275 Sorted by model distance: nonbonded pdb=" O ASP b 632 " pdb=" OG SER b 636 " model vdw 1.972 3.040 nonbonded pdb=" O THR C 278 " pdb=" O6 NAG q 1 " model vdw 2.058 3.040 nonbonded pdb=" OD2 ASP A 457 " pdb=" NH1 ARG A 469 " model vdw 2.113 3.120 nonbonded pdb=" NZ LYS C 169 " pdb=" OE2 GLU H 100N" model vdw 2.142 3.120 nonbonded pdb=" O THR A 278 " pdb=" O6 NAG X 1 " model vdw 2.144 3.040 ... (remaining 133270 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 605) selection = chain 'B' selection = (chain 'C' and (resid 33 through 397 or resid 411 through 605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'G' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'm' selection = chain 'q' } ncs_group { reference = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'R' and (resid 2 or resid 5 through 7)) selection = (chain 'p' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 1 or resid 4 through 6)) } ncs_group { reference = (chain 'a' and (resid 520 through 546 or resid 569 through 702)) selection = (chain 'b' and (resid 520 through 546 or resid 569 through 702)) selection = chain 'c' } 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: 5.110 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.750 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.003 0.052 17731 Z= 0.149 Angle : 0.640 13.541 24308 Z= 0.303 Chirality : 0.042 0.339 3061 Planarity : 0.003 0.052 2852 Dihedral : 10.404 83.301 8416 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.04 % Allowed : 3.92 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -1.46 (0.19), residues: 1933 helix: -1.48 (0.25), residues: 373 sheet: -0.46 (0.24), residues: 466 loop : -0.95 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 617 TYR 0.008 0.001 TYR L 32 PHE 0.008 0.001 PHE A 93 TRP 0.008 0.001 TRP B 69 HIS 0.004 0.001 HIS H 52A Details of bonding type rmsd covalent geometry : bond 0.00312 (17566) covalent geometry : angle 0.57911 (23849) SS BOND : bond 0.00183 ( 36) SS BOND : angle 0.88019 ( 72) hydrogen bonds : bond 0.26026 ( 537) hydrogen bonds : angle 8.99831 ( 1491) link_ALPHA1-2 : bond 0.01079 ( 4) link_ALPHA1-2 : angle 3.16460 ( 12) link_ALPHA1-3 : bond 0.01336 ( 9) link_ALPHA1-3 : angle 1.86874 ( 27) link_ALPHA1-6 : bond 0.01314 ( 6) link_ALPHA1-6 : angle 1.82150 ( 18) link_BETA1-3 : bond 0.00830 ( 1) link_BETA1-3 : angle 3.93756 ( 3) link_BETA1-4 : bond 0.00556 ( 49) link_BETA1-4 : angle 2.17598 ( 147) link_NAG-ASN : bond 0.00439 ( 60) link_NAG-ASN : angle 2.22153 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 308 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7762 (mtm-85) REVERT: C 335 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7608 (tttt) REVERT: A 296 CYS cc_start: 0.8491 (m) cc_final: 0.7744 (m) REVERT: B 35 TRP cc_start: 0.8146 (m-90) cc_final: 0.7759 (m100) REVERT: B 69 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7407 (p90) REVERT: B 82 GLN cc_start: 0.8290 (mp10) cc_final: 0.7921 (mp10) REVERT: B 125 LEU cc_start: 0.9017 (tp) cc_final: 0.8702 (tp) REVERT: B 174 SER cc_start: 0.9006 (t) cc_final: 0.8701 (m) REVERT: B 207 LYS cc_start: 0.8548 (mttt) cc_final: 0.8341 (mtpp) REVERT: c 616 ASN cc_start: 0.7933 (t0) cc_final: 0.7506 (t0) REVERT: c 632 ASP cc_start: 0.8684 (t70) cc_final: 0.8389 (t0) REVERT: c 640 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7784 (tm-30) REVERT: c 653 GLN cc_start: 0.7877 (tp40) cc_final: 0.7315 (mt0) REVERT: c 658 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7774 (tm-30) REVERT: a 601 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8748 (mtmm) REVERT: b 655 LYS cc_start: 0.7972 (tptp) cc_final: 0.7544 (ttpp) REVERT: H 59 GLN cc_start: 0.7729 (tp40) cc_final: 0.6811 (pp30) REVERT: H 60 LYS cc_start: 0.8070 (tptp) cc_final: 0.7731 (tttp) REVERT: H 101 TYR cc_start: 0.8433 (m-80) cc_final: 0.7979 (m-80) REVERT: L 46 LEU cc_start: 0.8276 (pt) cc_final: 0.7965 (pp) outliers start: 18 outliers final: 8 residues processed: 289 average time/residue: 0.1499 time to fit residues: 62.8445 Evaluate side-chains 179 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 GLN A 33 ASN A 67 ASN A 103 GLN A 249 HIS B 249 HIS B 330 HIS B 428 GLN c 630 GLN c 640 GLN a 543 ASN b 653 GLN L 53 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.163721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124136 restraints weight = 25429.998| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.74 r_work: 0.3406 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17731 Z= 0.198 Angle : 0.756 10.884 24308 Z= 0.351 Chirality : 0.049 0.380 3061 Planarity : 0.004 0.043 2852 Dihedral : 8.519 59.924 4763 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.73 % Allowed : 8.65 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.99 (0.19), residues: 1933 helix: -0.54 (0.26), residues: 392 sheet: -0.40 (0.22), residues: 515 loop : -0.75 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 617 TYR 0.020 0.002 TYR c 638 PHE 0.013 0.002 PHE B 317 TRP 0.014 0.001 TRP A 112 HIS 0.011 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00458 (17566) covalent geometry : angle 0.69223 (23849) SS BOND : bond 0.00252 ( 36) SS BOND : angle 1.34487 ( 72) hydrogen bonds : bond 0.05805 ( 537) hydrogen bonds : angle 5.85879 ( 1491) link_ALPHA1-2 : bond 0.00549 ( 4) link_ALPHA1-2 : angle 2.27689 ( 12) link_ALPHA1-3 : bond 0.01146 ( 9) link_ALPHA1-3 : angle 1.83557 ( 27) link_ALPHA1-6 : bond 0.00714 ( 6) link_ALPHA1-6 : angle 1.55321 ( 18) link_BETA1-3 : bond 0.01288 ( 1) link_BETA1-3 : angle 4.19156 ( 3) link_BETA1-4 : bond 0.00551 ( 49) link_BETA1-4 : angle 2.03512 ( 147) link_NAG-ASN : bond 0.00570 ( 60) link_NAG-ASN : angle 2.86507 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 308 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7871 (mtm-85) REVERT: A 173 TYR cc_start: 0.8241 (p90) cc_final: 0.7983 (p90) REVERT: A 209 SER cc_start: 0.8773 (t) cc_final: 0.8366 (p) REVERT: B 35 TRP cc_start: 0.8294 (m-90) cc_final: 0.7977 (m100) REVERT: B 69 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7567 (p90) REVERT: B 82 GLN cc_start: 0.8310 (mp10) cc_final: 0.8043 (mp10) REVERT: B 125 LEU cc_start: 0.9135 (tp) cc_final: 0.8828 (tp) REVERT: B 207 LYS cc_start: 0.8731 (mttt) cc_final: 0.8464 (mtpp) REVERT: c 616 ASN cc_start: 0.7709 (t0) cc_final: 0.7348 (t0) REVERT: c 632 ASP cc_start: 0.8594 (t70) cc_final: 0.8254 (t0) REVERT: c 653 GLN cc_start: 0.8037 (tp40) cc_final: 0.7607 (mt0) REVERT: c 658 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8132 (tm-30) REVERT: a 601 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8738 (mtmm) REVERT: a 634 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8267 (mt-10) REVERT: b 655 LYS cc_start: 0.8166 (tptp) cc_final: 0.7772 (ttpt) REVERT: H 52 GLU cc_start: 0.8020 (mp0) cc_final: 0.7740 (mp0) REVERT: H 59 GLN cc_start: 0.7680 (tp40) cc_final: 0.6860 (pp30) REVERT: H 60 LYS cc_start: 0.8002 (tptp) cc_final: 0.7679 (tttp) REVERT: H 93 LEU cc_start: 0.7193 (pp) cc_final: 0.6945 (pp) REVERT: H 101 TYR cc_start: 0.8629 (m-80) cc_final: 0.8332 (m-80) REVERT: L 46 LEU cc_start: 0.8304 (pt) cc_final: 0.7960 (pp) REVERT: L 93 HIS cc_start: 0.6173 (m-70) cc_final: 0.5901 (m-70) outliers start: 30 outliers final: 18 residues processed: 209 average time/residue: 0.1261 time to fit residues: 40.2535 Evaluate side-chains 185 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain b residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 chunk 73 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN c 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113837 restraints weight = 25512.674| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.32 r_work: 0.3304 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17731 Z= 0.124 Angle : 0.688 12.497 24308 Z= 0.313 Chirality : 0.047 0.353 3061 Planarity : 0.004 0.040 2852 Dihedral : 8.275 59.678 4759 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.02 % Allowed : 9.57 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.71 (0.19), residues: 1933 helix: -0.09 (0.27), residues: 391 sheet: -0.37 (0.22), residues: 513 loop : -0.58 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.032 0.001 TYR H 79 PHE 0.009 0.001 PHE B 317 TRP 0.011 0.001 TRP L 35 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00263 (17566) covalent geometry : angle 0.61235 (23849) SS BOND : bond 0.00209 ( 36) SS BOND : angle 1.67899 ( 72) hydrogen bonds : bond 0.04775 ( 537) hydrogen bonds : angle 5.32232 ( 1491) link_ALPHA1-2 : bond 0.00495 ( 4) link_ALPHA1-2 : angle 2.14146 ( 12) link_ALPHA1-3 : bond 0.01151 ( 9) link_ALPHA1-3 : angle 1.76959 ( 27) link_ALPHA1-6 : bond 0.00757 ( 6) link_ALPHA1-6 : angle 1.52261 ( 18) link_BETA1-3 : bond 0.01126 ( 1) link_BETA1-3 : angle 3.93957 ( 3) link_BETA1-4 : bond 0.00520 ( 49) link_BETA1-4 : angle 1.96305 ( 147) link_NAG-ASN : bond 0.00545 ( 60) link_NAG-ASN : angle 2.95536 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8254 (tpp) cc_final: 0.8032 (tpp) REVERT: C 308 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: C 486 TYR cc_start: 0.8885 (m-80) cc_final: 0.8615 (m-80) REVERT: A 173 TYR cc_start: 0.8229 (p90) cc_final: 0.7990 (p90) REVERT: A 192 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7675 (ptt-90) REVERT: A 195 ASN cc_start: 0.8940 (p0) cc_final: 0.8718 (p0) REVERT: A 207 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7619 (tptt) REVERT: A 209 SER cc_start: 0.8751 (t) cc_final: 0.8318 (p) REVERT: B 35 TRP cc_start: 0.8248 (m-90) cc_final: 0.7939 (m100) REVERT: B 69 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.7248 (p90) REVERT: B 125 LEU cc_start: 0.9094 (tp) cc_final: 0.8746 (tp) REVERT: B 207 LYS cc_start: 0.8592 (mttt) cc_final: 0.8323 (mtpp) REVERT: c 571 TRP cc_start: 0.7606 (m100) cc_final: 0.7381 (m100) REVERT: c 616 ASN cc_start: 0.7696 (t0) cc_final: 0.7307 (t0) REVERT: c 632 ASP cc_start: 0.8578 (t70) cc_final: 0.8272 (t0) REVERT: c 635 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8168 (mm) REVERT: c 653 GLN cc_start: 0.7968 (tp40) cc_final: 0.7588 (mt0) REVERT: a 601 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8655 (mtmm) REVERT: a 634 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8200 (mt-10) REVERT: b 626 MET cc_start: 0.8379 (mtp) cc_final: 0.8129 (mtp) REVERT: b 637 ASN cc_start: 0.7507 (m-40) cc_final: 0.7158 (m-40) REVERT: b 655 LYS cc_start: 0.8151 (tptp) cc_final: 0.7689 (ttpp) REVERT: H 52 GLU cc_start: 0.8097 (mp0) cc_final: 0.7853 (mp0) REVERT: H 59 GLN cc_start: 0.7737 (tp40) cc_final: 0.6891 (pp30) REVERT: H 60 LYS cc_start: 0.8029 (tptp) cc_final: 0.7695 (tttp) REVERT: H 101 TYR cc_start: 0.8572 (m-80) cc_final: 0.8274 (m-80) REVERT: L 46 LEU cc_start: 0.8379 (pt) cc_final: 0.8132 (pp) outliers start: 35 outliers final: 21 residues processed: 216 average time/residue: 0.1350 time to fit residues: 44.5982 Evaluate side-chains 197 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 103 GLN B 183 GLN H 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113458 restraints weight = 25433.576| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.29 r_work: 0.3301 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17731 Z= 0.130 Angle : 0.663 10.523 24308 Z= 0.300 Chirality : 0.046 0.363 3061 Planarity : 0.003 0.041 2852 Dihedral : 8.222 59.323 4759 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.36 % Allowed : 10.72 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.54 (0.19), residues: 1933 helix: 0.18 (0.27), residues: 392 sheet: -0.33 (0.21), residues: 544 loop : -0.49 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 542 TYR 0.019 0.001 TYR H 79 PHE 0.010 0.001 PHE B 317 TRP 0.012 0.001 TRP H 36 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00290 (17566) covalent geometry : angle 0.59421 (23849) SS BOND : bond 0.00204 ( 36) SS BOND : angle 1.27283 ( 72) hydrogen bonds : bond 0.04226 ( 537) hydrogen bonds : angle 5.04783 ( 1491) link_ALPHA1-2 : bond 0.00462 ( 4) link_ALPHA1-2 : angle 2.02307 ( 12) link_ALPHA1-3 : bond 0.01081 ( 9) link_ALPHA1-3 : angle 1.74455 ( 27) link_ALPHA1-6 : bond 0.00717 ( 6) link_ALPHA1-6 : angle 1.51945 ( 18) link_BETA1-3 : bond 0.01133 ( 1) link_BETA1-3 : angle 3.81397 ( 3) link_BETA1-4 : bond 0.00529 ( 49) link_BETA1-4 : angle 1.85507 ( 147) link_NAG-ASN : bond 0.00541 ( 60) link_NAG-ASN : angle 2.82967 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7531 (mt0) cc_final: 0.7204 (tp40) REVERT: A 192 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7639 (ptt-90) REVERT: A 207 LYS cc_start: 0.7904 (ptmm) cc_final: 0.7563 (tptt) REVERT: A 209 SER cc_start: 0.8754 (t) cc_final: 0.8313 (p) REVERT: B 35 TRP cc_start: 0.8270 (m-90) cc_final: 0.7933 (m100) REVERT: B 69 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.6890 (p90) REVERT: B 125 LEU cc_start: 0.9100 (tp) cc_final: 0.8730 (tp) REVERT: B 207 LYS cc_start: 0.8643 (mttt) cc_final: 0.8390 (mtpp) REVERT: c 616 ASN cc_start: 0.7567 (t0) cc_final: 0.7157 (t0) REVERT: c 632 ASP cc_start: 0.8497 (t70) cc_final: 0.8222 (t0) REVERT: c 635 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7777 (mm) REVERT: c 653 GLN cc_start: 0.8036 (tp40) cc_final: 0.7584 (mt0) REVERT: a 588 ARG cc_start: 0.8066 (ttp-170) cc_final: 0.7727 (ttm110) REVERT: a 601 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8787 (mtmm) REVERT: a 634 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8161 (mt-10) REVERT: b 626 MET cc_start: 0.8409 (mtp) cc_final: 0.8155 (mtp) REVERT: b 637 ASN cc_start: 0.7450 (m-40) cc_final: 0.7140 (m-40) REVERT: b 655 LYS cc_start: 0.8046 (tptp) cc_final: 0.7642 (ttpp) REVERT: H 52 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: H 59 GLN cc_start: 0.7753 (tp40) cc_final: 0.6898 (pp30) REVERT: H 60 LYS cc_start: 0.7989 (tptp) cc_final: 0.7668 (tttp) REVERT: H 101 TYR cc_start: 0.8578 (m-80) cc_final: 0.8240 (m-80) REVERT: L 46 LEU cc_start: 0.8422 (pt) cc_final: 0.8197 (pp) outliers start: 41 outliers final: 25 residues processed: 216 average time/residue: 0.1402 time to fit residues: 46.0079 Evaluate side-chains 201 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112440 restraints weight = 25404.209| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.29 r_work: 0.3306 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17731 Z= 0.132 Angle : 0.657 10.938 24308 Z= 0.298 Chirality : 0.046 0.364 3061 Planarity : 0.003 0.041 2852 Dihedral : 8.193 72.083 4754 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.07 % Allowed : 11.59 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 1933 helix: 0.31 (0.27), residues: 397 sheet: -0.23 (0.21), residues: 531 loop : -0.46 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 542 TYR 0.021 0.001 TYR a 638 PHE 0.016 0.001 PHE B 53 TRP 0.011 0.001 TRP B 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00300 (17566) covalent geometry : angle 0.58951 (23849) SS BOND : bond 0.00214 ( 36) SS BOND : angle 1.35408 ( 72) hydrogen bonds : bond 0.04026 ( 537) hydrogen bonds : angle 4.84825 ( 1491) link_ALPHA1-2 : bond 0.00435 ( 4) link_ALPHA1-2 : angle 1.93107 ( 12) link_ALPHA1-3 : bond 0.01054 ( 9) link_ALPHA1-3 : angle 1.74214 ( 27) link_ALPHA1-6 : bond 0.00709 ( 6) link_ALPHA1-6 : angle 1.51519 ( 18) link_BETA1-3 : bond 0.01133 ( 1) link_BETA1-3 : angle 3.60160 ( 3) link_BETA1-4 : bond 0.00534 ( 49) link_BETA1-4 : angle 1.83795 ( 147) link_NAG-ASN : bond 0.00466 ( 60) link_NAG-ASN : angle 2.75773 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7528 (mt0) cc_final: 0.7241 (tp40) REVERT: C 308 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7722 (mtm-85) REVERT: A 192 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7626 (ptt-90) REVERT: A 195 ASN cc_start: 0.8914 (p0) cc_final: 0.8671 (p0) REVERT: A 207 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7544 (tptt) REVERT: A 209 SER cc_start: 0.8766 (t) cc_final: 0.8344 (p) REVERT: B 35 TRP cc_start: 0.8290 (m-90) cc_final: 0.7986 (m100) REVERT: B 125 LEU cc_start: 0.9092 (tp) cc_final: 0.8691 (tp) REVERT: B 174 SER cc_start: 0.8993 (t) cc_final: 0.8715 (m) REVERT: B 207 LYS cc_start: 0.8646 (mttt) cc_final: 0.8409 (mtpp) REVERT: c 616 ASN cc_start: 0.7502 (t0) cc_final: 0.7094 (t0) REVERT: c 632 ASP cc_start: 0.8503 (t70) cc_final: 0.8236 (t0) REVERT: c 635 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7756 (mm) REVERT: c 653 GLN cc_start: 0.8073 (tp40) cc_final: 0.7651 (mt0) REVERT: c 658 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7895 (tp40) REVERT: a 588 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7715 (ttm110) REVERT: a 601 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8676 (mtmm) REVERT: a 634 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8119 (mt-10) REVERT: b 626 MET cc_start: 0.8457 (mtp) cc_final: 0.8199 (mtp) REVERT: b 632 ASP cc_start: 0.8542 (t0) cc_final: 0.8274 (t0) REVERT: b 655 LYS cc_start: 0.8029 (tptp) cc_final: 0.7634 (ttpp) REVERT: H 51 MET cc_start: 0.6707 (ttt) cc_final: 0.6138 (ttt) REVERT: H 52 GLU cc_start: 0.8226 (mp0) cc_final: 0.7927 (mp0) REVERT: H 60 LYS cc_start: 0.7971 (tptp) cc_final: 0.7665 (tttp) REVERT: H 101 TYR cc_start: 0.8572 (m-80) cc_final: 0.8242 (m-80) REVERT: H 104 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8407 (t) REVERT: L 46 LEU cc_start: 0.8402 (pt) cc_final: 0.8173 (pp) REVERT: L 96 TRP cc_start: 0.7782 (m-90) cc_final: 0.6886 (m-90) outliers start: 36 outliers final: 24 residues processed: 210 average time/residue: 0.1429 time to fit residues: 46.0487 Evaluate side-chains 203 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 125 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 625 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110008 restraints weight = 25707.767| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.17 r_work: 0.3259 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17731 Z= 0.238 Angle : 0.745 11.712 24308 Z= 0.339 Chirality : 0.049 0.387 3061 Planarity : 0.004 0.043 2852 Dihedral : 8.583 59.942 4751 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.88 % Allowed : 11.53 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.78 (0.19), residues: 1933 helix: -0.04 (0.27), residues: 404 sheet: -0.43 (0.21), residues: 555 loop : -0.68 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 542 TYR 0.023 0.002 TYR a 638 PHE 0.015 0.002 PHE B 317 TRP 0.015 0.001 TRP B 112 HIS 0.005 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00568 (17566) covalent geometry : angle 0.68247 (23849) SS BOND : bond 0.00291 ( 36) SS BOND : angle 1.45513 ( 72) hydrogen bonds : bond 0.04564 ( 537) hydrogen bonds : angle 5.07478 ( 1491) link_ALPHA1-2 : bond 0.00410 ( 4) link_ALPHA1-2 : angle 2.02856 ( 12) link_ALPHA1-3 : bond 0.00998 ( 9) link_ALPHA1-3 : angle 1.72298 ( 27) link_ALPHA1-6 : bond 0.00644 ( 6) link_ALPHA1-6 : angle 1.61190 ( 18) link_BETA1-3 : bond 0.01219 ( 1) link_BETA1-3 : angle 3.47493 ( 3) link_BETA1-4 : bond 0.00521 ( 49) link_BETA1-4 : angle 1.85655 ( 147) link_NAG-ASN : bond 0.00585 ( 60) link_NAG-ASN : angle 2.88824 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7636 (mt0) cc_final: 0.7348 (tp40) REVERT: C 356 ASN cc_start: 0.8380 (t0) cc_final: 0.8165 (t0) REVERT: A 173 TYR cc_start: 0.8354 (p90) cc_final: 0.8042 (p90) REVERT: A 192 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7694 (ptt-90) REVERT: A 207 LYS cc_start: 0.7886 (ptmm) cc_final: 0.7592 (tptt) REVERT: A 209 SER cc_start: 0.8868 (t) cc_final: 0.8429 (p) REVERT: B 35 TRP cc_start: 0.8321 (m-90) cc_final: 0.7967 (m100) REVERT: B 125 LEU cc_start: 0.9171 (tp) cc_final: 0.8705 (tp) REVERT: B 174 SER cc_start: 0.8999 (t) cc_final: 0.8723 (m) REVERT: B 207 LYS cc_start: 0.8699 (mttt) cc_final: 0.8436 (mtpp) REVERT: B 368 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7645 (p0) REVERT: c 616 ASN cc_start: 0.7537 (t0) cc_final: 0.7155 (t0) REVERT: c 632 ASP cc_start: 0.8586 (t70) cc_final: 0.8316 (t0) REVERT: c 635 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7700 (mm) REVERT: c 653 GLN cc_start: 0.8133 (tp40) cc_final: 0.7680 (mt0) REVERT: c 658 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7750 (tp40) REVERT: a 588 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7715 (ttm110) REVERT: a 601 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8686 (mtmm) REVERT: a 634 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8143 (mt-10) REVERT: b 626 MET cc_start: 0.8468 (mtp) cc_final: 0.8223 (mtp) REVERT: b 632 ASP cc_start: 0.8649 (t0) cc_final: 0.8414 (t0) REVERT: b 655 LYS cc_start: 0.8121 (tptp) cc_final: 0.7647 (ttpp) REVERT: H 52 GLU cc_start: 0.8320 (mp0) cc_final: 0.7669 (mp0) REVERT: H 101 TYR cc_start: 0.8606 (m-80) cc_final: 0.8161 (m-80) REVERT: H 104 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (t) REVERT: L 46 LEU cc_start: 0.8364 (pt) cc_final: 0.8135 (pp) REVERT: L 96 TRP cc_start: 0.7793 (m-90) cc_final: 0.6964 (m-90) outliers start: 50 outliers final: 37 residues processed: 205 average time/residue: 0.1328 time to fit residues: 41.6059 Evaluate side-chains 204 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 626 MET Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 172 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 95 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112311 restraints weight = 25462.289| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.23 r_work: 0.3297 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17731 Z= 0.129 Angle : 0.660 11.658 24308 Z= 0.298 Chirality : 0.046 0.372 3061 Planarity : 0.003 0.043 2852 Dihedral : 8.284 59.940 4751 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.77 % Allowed : 11.82 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.53 (0.19), residues: 1933 helix: 0.33 (0.27), residues: 395 sheet: -0.34 (0.21), residues: 551 loop : -0.54 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 542 TYR 0.020 0.001 TYR a 638 PHE 0.012 0.001 PHE B 53 TRP 0.013 0.001 TRP B 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00289 (17566) covalent geometry : angle 0.59554 (23849) SS BOND : bond 0.00213 ( 36) SS BOND : angle 1.23127 ( 72) hydrogen bonds : bond 0.03960 ( 537) hydrogen bonds : angle 4.81091 ( 1491) link_ALPHA1-2 : bond 0.00431 ( 4) link_ALPHA1-2 : angle 1.88089 ( 12) link_ALPHA1-3 : bond 0.01059 ( 9) link_ALPHA1-3 : angle 1.70565 ( 27) link_ALPHA1-6 : bond 0.00717 ( 6) link_ALPHA1-6 : angle 1.51079 ( 18) link_BETA1-3 : bond 0.01128 ( 1) link_BETA1-3 : angle 3.31270 ( 3) link_BETA1-4 : bond 0.00493 ( 49) link_BETA1-4 : angle 1.79168 ( 147) link_NAG-ASN : bond 0.00526 ( 60) link_NAG-ASN : angle 2.74220 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7606 (mt0) cc_final: 0.7313 (tp40) REVERT: C 308 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: C 356 ASN cc_start: 0.8325 (t0) cc_final: 0.8116 (t0) REVERT: A 173 TYR cc_start: 0.8332 (p90) cc_final: 0.8000 (p90) REVERT: A 192 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7659 (ptt-90) REVERT: A 195 ASN cc_start: 0.8897 (p0) cc_final: 0.8650 (p0) REVERT: A 207 LYS cc_start: 0.7878 (ptmm) cc_final: 0.7531 (tptt) REVERT: A 209 SER cc_start: 0.8860 (t) cc_final: 0.8414 (p) REVERT: B 35 TRP cc_start: 0.8304 (m-90) cc_final: 0.7946 (m100) REVERT: B 125 LEU cc_start: 0.9062 (tp) cc_final: 0.8662 (tp) REVERT: B 207 LYS cc_start: 0.8719 (mttt) cc_final: 0.8465 (mtpp) REVERT: B 368 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7631 (p0) REVERT: c 616 ASN cc_start: 0.7441 (t0) cc_final: 0.7069 (t0) REVERT: c 632 ASP cc_start: 0.8485 (t70) cc_final: 0.8210 (t0) REVERT: c 635 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7659 (mm) REVERT: c 653 GLN cc_start: 0.8085 (tp40) cc_final: 0.7714 (mt0) REVERT: c 658 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7568 (tp40) REVERT: a 601 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8767 (mtmm) REVERT: a 634 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8096 (mt-10) REVERT: b 626 MET cc_start: 0.8465 (mtp) cc_final: 0.8214 (mtp) REVERT: b 632 ASP cc_start: 0.8568 (t0) cc_final: 0.8265 (t0) REVERT: b 655 LYS cc_start: 0.8126 (tptp) cc_final: 0.7699 (ttpp) REVERT: H 104 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8367 (t) REVERT: L 46 LEU cc_start: 0.8374 (pt) cc_final: 0.8162 (pp) REVERT: L 96 TRP cc_start: 0.7781 (m-90) cc_final: 0.7046 (m-90) outliers start: 48 outliers final: 35 residues processed: 207 average time/residue: 0.1373 time to fit residues: 43.6583 Evaluate side-chains 204 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 84 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112615 restraints weight = 25574.110| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.17 r_work: 0.3308 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17731 Z= 0.123 Angle : 0.651 11.097 24308 Z= 0.295 Chirality : 0.046 0.369 3061 Planarity : 0.003 0.045 2852 Dihedral : 8.126 59.656 4751 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.82 % Allowed : 12.05 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.38 (0.19), residues: 1933 helix: 0.45 (0.27), residues: 398 sheet: -0.15 (0.22), residues: 529 loop : -0.51 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 542 TYR 0.023 0.001 TYR a 638 PHE 0.011 0.001 PHE B 53 TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00273 (17566) covalent geometry : angle 0.58941 (23849) SS BOND : bond 0.00214 ( 36) SS BOND : angle 1.28923 ( 72) hydrogen bonds : bond 0.03805 ( 537) hydrogen bonds : angle 4.68587 ( 1491) link_ALPHA1-2 : bond 0.00409 ( 4) link_ALPHA1-2 : angle 1.82747 ( 12) link_ALPHA1-3 : bond 0.01032 ( 9) link_ALPHA1-3 : angle 1.69974 ( 27) link_ALPHA1-6 : bond 0.00722 ( 6) link_ALPHA1-6 : angle 1.49585 ( 18) link_BETA1-3 : bond 0.01121 ( 1) link_BETA1-3 : angle 3.25219 ( 3) link_BETA1-4 : bond 0.00519 ( 49) link_BETA1-4 : angle 1.77532 ( 147) link_NAG-ASN : bond 0.00548 ( 60) link_NAG-ASN : angle 2.64417 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7613 (mt0) cc_final: 0.7322 (tp40) REVERT: A 173 TYR cc_start: 0.8308 (p90) cc_final: 0.7993 (p90) REVERT: A 192 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7623 (ptt-90) REVERT: A 195 ASN cc_start: 0.8876 (p0) cc_final: 0.8613 (p0) REVERT: A 207 LYS cc_start: 0.7863 (ptmm) cc_final: 0.7538 (tptt) REVERT: A 209 SER cc_start: 0.8842 (t) cc_final: 0.8400 (p) REVERT: B 35 TRP cc_start: 0.8299 (m-90) cc_final: 0.7936 (m100) REVERT: B 125 LEU cc_start: 0.9049 (tp) cc_final: 0.8647 (tp) REVERT: B 207 LYS cc_start: 0.8715 (mttt) cc_final: 0.8464 (mtpp) REVERT: B 368 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7593 (p0) REVERT: c 616 ASN cc_start: 0.7432 (t0) cc_final: 0.7063 (t0) REVERT: c 632 ASP cc_start: 0.8450 (t70) cc_final: 0.8199 (t0) REVERT: c 635 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7508 (mm) REVERT: c 653 GLN cc_start: 0.8101 (tp40) cc_final: 0.7755 (mt0) REVERT: a 601 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8721 (mtmm) REVERT: a 634 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8079 (mt-10) REVERT: b 632 ASP cc_start: 0.8574 (t0) cc_final: 0.8246 (t0) REVERT: b 655 LYS cc_start: 0.8117 (tptp) cc_final: 0.7674 (ttpp) REVERT: H 52 GLU cc_start: 0.8508 (mp0) cc_final: 0.8268 (mp0) REVERT: H 104 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8365 (t) REVERT: L 46 LEU cc_start: 0.8308 (pt) cc_final: 0.8097 (pp) REVERT: L 96 TRP cc_start: 0.7778 (m-90) cc_final: 0.7070 (m-90) outliers start: 49 outliers final: 38 residues processed: 206 average time/residue: 0.1435 time to fit residues: 44.8769 Evaluate side-chains 206 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 12 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 89 optimal weight: 0.0060 chunk 151 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114122 restraints weight = 25551.531| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.29 r_work: 0.3319 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17731 Z= 0.106 Angle : 0.633 11.140 24308 Z= 0.288 Chirality : 0.045 0.362 3061 Planarity : 0.003 0.045 2852 Dihedral : 7.901 59.923 4751 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.36 % Allowed : 12.85 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.19 (0.19), residues: 1933 helix: 0.88 (0.28), residues: 382 sheet: -0.07 (0.22), residues: 518 loop : -0.47 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 542 TYR 0.020 0.001 TYR a 638 PHE 0.027 0.001 PHE H 61 TRP 0.010 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00227 (17566) covalent geometry : angle 0.57269 (23849) SS BOND : bond 0.00201 ( 36) SS BOND : angle 1.19434 ( 72) hydrogen bonds : bond 0.03515 ( 537) hydrogen bonds : angle 4.52798 ( 1491) link_ALPHA1-2 : bond 0.00439 ( 4) link_ALPHA1-2 : angle 1.72439 ( 12) link_ALPHA1-3 : bond 0.01029 ( 9) link_ALPHA1-3 : angle 1.69277 ( 27) link_ALPHA1-6 : bond 0.00757 ( 6) link_ALPHA1-6 : angle 1.47560 ( 18) link_BETA1-3 : bond 0.01095 ( 1) link_BETA1-3 : angle 3.17556 ( 3) link_BETA1-4 : bond 0.00503 ( 49) link_BETA1-4 : angle 1.70025 ( 147) link_NAG-ASN : bond 0.00557 ( 60) link_NAG-ASN : angle 2.59598 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7639 (mt0) cc_final: 0.7348 (tp40) REVERT: C 308 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7721 (mtm-85) REVERT: A 192 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7592 (ptt-90) REVERT: A 195 ASN cc_start: 0.8889 (p0) cc_final: 0.8629 (p0) REVERT: A 207 LYS cc_start: 0.7832 (ptmm) cc_final: 0.7455 (tptt) REVERT: A 209 SER cc_start: 0.8791 (t) cc_final: 0.8343 (p) REVERT: B 35 TRP cc_start: 0.8288 (m-90) cc_final: 0.7902 (m100) REVERT: B 125 LEU cc_start: 0.9012 (tp) cc_final: 0.8609 (tp) REVERT: B 207 LYS cc_start: 0.8712 (mttt) cc_final: 0.8461 (mtpp) REVERT: c 535 MET cc_start: 0.8777 (tpp) cc_final: 0.8488 (tpp) REVERT: c 616 ASN cc_start: 0.7377 (t0) cc_final: 0.7018 (t0) REVERT: c 635 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7531 (mm) REVERT: c 653 GLN cc_start: 0.8095 (tp40) cc_final: 0.7766 (mt0) REVERT: a 601 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8699 (mtmm) REVERT: a 634 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8092 (mt-10) REVERT: b 632 ASP cc_start: 0.8618 (t0) cc_final: 0.8268 (t0) REVERT: b 655 LYS cc_start: 0.8019 (tptp) cc_final: 0.7640 (ttpp) REVERT: H 104 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8405 (t) REVERT: L 46 LEU cc_start: 0.8310 (pt) cc_final: 0.8108 (pp) REVERT: L 96 TRP cc_start: 0.7753 (m-90) cc_final: 0.7223 (m-90) outliers start: 41 outliers final: 35 residues processed: 212 average time/residue: 0.1435 time to fit residues: 45.8740 Evaluate side-chains 209 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 618 ASN Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain b residue 636 SER Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 164 optimal weight: 0.0470 chunk 178 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN C 356 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 630 GLN a 543 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114618 restraints weight = 25317.412| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.17 r_work: 0.3335 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17731 Z= 0.110 Angle : 0.637 10.867 24308 Z= 0.291 Chirality : 0.045 0.362 3061 Planarity : 0.003 0.045 2852 Dihedral : 7.823 59.618 4751 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.19 % Allowed : 13.03 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.13 (0.19), residues: 1933 helix: 1.05 (0.28), residues: 379 sheet: -0.07 (0.22), residues: 524 loop : -0.46 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 542 TYR 0.020 0.001 TYR a 638 PHE 0.022 0.001 PHE H 61 TRP 0.010 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00237 (17566) covalent geometry : angle 0.57991 (23849) SS BOND : bond 0.00191 ( 36) SS BOND : angle 1.15312 ( 72) hydrogen bonds : bond 0.03462 ( 537) hydrogen bonds : angle 4.45704 ( 1491) link_ALPHA1-2 : bond 0.00430 ( 4) link_ALPHA1-2 : angle 1.68680 ( 12) link_ALPHA1-3 : bond 0.00998 ( 9) link_ALPHA1-3 : angle 1.67698 ( 27) link_ALPHA1-6 : bond 0.00744 ( 6) link_ALPHA1-6 : angle 1.46210 ( 18) link_BETA1-3 : bond 0.01099 ( 1) link_BETA1-3 : angle 3.14013 ( 3) link_BETA1-4 : bond 0.00532 ( 49) link_BETA1-4 : angle 1.72866 ( 147) link_NAG-ASN : bond 0.00586 ( 60) link_NAG-ASN : angle 2.49244 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: C 246 GLN cc_start: 0.7585 (mt0) cc_final: 0.7335 (tp40) REVERT: C 308 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: A 192 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7558 (ptt-90) REVERT: A 195 ASN cc_start: 0.8868 (p0) cc_final: 0.8611 (p0) REVERT: A 207 LYS cc_start: 0.7813 (ptmm) cc_final: 0.7459 (tptt) REVERT: A 209 SER cc_start: 0.8791 (t) cc_final: 0.8328 (p) REVERT: B 35 TRP cc_start: 0.8284 (m-90) cc_final: 0.7899 (m100) REVERT: B 125 LEU cc_start: 0.8970 (tp) cc_final: 0.8571 (tp) REVERT: B 207 LYS cc_start: 0.8699 (mttt) cc_final: 0.8452 (mtpp) REVERT: c 535 MET cc_start: 0.8744 (tpp) cc_final: 0.8449 (tpp) REVERT: c 635 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7462 (mm) REVERT: c 653 GLN cc_start: 0.8094 (tp40) cc_final: 0.7764 (mt0) REVERT: a 601 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8701 (mtmm) REVERT: a 634 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8047 (mt-10) REVERT: b 632 ASP cc_start: 0.8605 (t0) cc_final: 0.8238 (t0) REVERT: b 655 LYS cc_start: 0.8052 (tptp) cc_final: 0.7655 (ttpp) REVERT: H 60 LYS cc_start: 0.7750 (tttm) cc_final: 0.7161 (tptp) REVERT: H 104 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8380 (t) REVERT: L 46 LEU cc_start: 0.8283 (pt) cc_final: 0.8065 (pp) REVERT: L 96 TRP cc_start: 0.7711 (m-90) cc_final: 0.7205 (m-90) outliers start: 38 outliers final: 34 residues processed: 208 average time/residue: 0.1423 time to fit residues: 44.6579 Evaluate side-chains 210 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain c residue 619 LEU Chi-restraints excluded: chain c residue 627 THR Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 639 THR Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain b residue 641 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 185 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN a 543 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112710 restraints weight = 25477.117| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.15 r_work: 0.3309 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17731 Z= 0.144 Angle : 0.668 11.307 24308 Z= 0.303 Chirality : 0.046 0.371 3061 Planarity : 0.003 0.046 2852 Dihedral : 7.951 59.767 4751 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 13.20 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.18 (0.19), residues: 1933 helix: 0.99 (0.28), residues: 375 sheet: -0.10 (0.22), residues: 526 loop : -0.48 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 542 TYR 0.054 0.002 TYR b 638 PHE 0.016 0.001 PHE H 61 TRP 0.012 0.001 TRP b 596 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00330 (17566) covalent geometry : angle 0.60576 (23849) SS BOND : bond 0.00217 ( 36) SS BOND : angle 1.22960 ( 72) hydrogen bonds : bond 0.03800 ( 537) hydrogen bonds : angle 4.51522 ( 1491) link_ALPHA1-2 : bond 0.00398 ( 4) link_ALPHA1-2 : angle 1.74224 ( 12) link_ALPHA1-3 : bond 0.00967 ( 9) link_ALPHA1-3 : angle 1.66617 ( 27) link_ALPHA1-6 : bond 0.00710 ( 6) link_ALPHA1-6 : angle 1.51508 ( 18) link_BETA1-3 : bond 0.01137 ( 1) link_BETA1-3 : angle 3.10054 ( 3) link_BETA1-4 : bond 0.00521 ( 49) link_BETA1-4 : angle 1.72926 ( 147) link_NAG-ASN : bond 0.00555 ( 60) link_NAG-ASN : angle 2.75467 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.50 seconds wall clock time: 66 minutes 35.83 seconds (3995.83 seconds total)