Starting phenix.real_space_refine on Thu Sep 18 13:42:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.map" model { file = "/net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d7o_46613/09_2025/9d7o_46613.cif" } resolution = 3.56 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 10730 2.51 5 N 2845 2.21 5 O 3470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 17163 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 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: "C" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3388 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 976 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 2 Chain: "E" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3455 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1254 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 13, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1320 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: 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: "i" 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: "o" 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: "A" 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.85, per 1000 atoms: 0.22 Number of scatterers: 17163 At special positions: 0 Unit cell: (133.92, 155.52, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 3470 8.00 N 2845 7.00 C 10730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " 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 149 " 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 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.06 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 149 " 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=2.09 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 193 " 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 BETA1-4 " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 197 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 392 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 448 " " NAG K 1 " - " ASN A 88 " " NAG L 1 " - " ASN A 148 " " NAG M 1 " - " ASN A 152 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN C 88 " " NAG U 1 " - " ASN C 148 " " NAG V 1 " - " ASN C 152 " " NAG W 1 " - " ASN C 234 " " NAG X 1 " - " ASN C 262 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 295 " " NAG a 1 " - " ASN C 301 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 448 " " NAG f 1 " - " ASN E 88 " " NAG g 1 " - " ASN E 148 " " NAG h 1 " - " ASN E 152 " " NAG i 1 " - " ASN E 262 " " NAG j 1 " - " ASN E 276 " " NAG k 1 " - " ASN E 295 " " NAG l 1 " - " ASN E 301 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 363 " " NAG o 1 " - " ASN E 386 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 707.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 38 sheets defined 19.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.746A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.574A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.846A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.705A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 531 through 535' Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.185A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.651A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.039A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.715A pdb=" N VAL C 75 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 335 through 350 removed outlier: 5.088A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 4.243A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.517A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 639 through 663 removed outlier: 4.008A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.844A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.697A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.662A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.420A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.432A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.716A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.720A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.582A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA2, first strand: chain 'A' and resid 494 through 495 removed outlier: 4.208A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.577A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.071A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.747A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.911A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 161 through 168 removed outlier: 3.751A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.938A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.936A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.101A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 283 through 302 current: chain 'A' and resid 358 through 361 removed outlier: 3.636A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.101A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.936A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 457 current: chain 'A' and resid 413 through 414 Processing sheet with id=AB1, first strand: chain 'A' and resid 307 through 312 removed outlier: 3.582A pdb=" N ILE A 309 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.432A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.397A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.112A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.682A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AB8, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB9, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.464A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.046A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.420A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.492A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.482A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 332 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 416 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 271 through 274 removed outlier: 12.482A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.492A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.420A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 304 through 308 removed outlier: 3.512A pdb=" N LYS C 305 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 3.513A pdb=" N TRP E 35 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.045A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.521A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 161 through 169 removed outlier: 3.715A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 removed outlier: 5.681A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS E 445 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.451A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.741A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.675A pdb=" N CYS G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 47 " --> pdb=" O TRP G 35 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AD6, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=AD7, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.685A pdb=" N PHE G 118 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.685A pdb=" N PHE G 118 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.362A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 121 through 122 removed outlier: 3.757A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1473 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: 3.00 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5315 1.35 - 1.48: 4609 1.48 - 1.61: 7408 1.61 - 1.75: 1 1.75 - 1.88: 155 Bond restraints: 17488 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.380 -0.048 7.90e-03 1.60e+04 3.73e+01 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.390 -0.055 9.40e-03 1.13e+04 3.46e+01 bond pdb=" C LYS H 201 " pdb=" N PRO H 202 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.20e-02 6.94e+03 1.33e+01 bond pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.59e+00 bond pdb=" N CYS C 74 " pdb=" CA CYS C 74 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.93e+00 ... (remaining 17483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 23626 4.75 - 9.49: 107 9.49 - 14.24: 9 14.24 - 18.98: 1 18.98 - 23.73: 1 Bond angle restraints: 23744 Sorted by residual: angle pdb=" CA CYS C 331 " pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 114.40 138.13 -23.73 2.30e+00 1.89e-01 1.06e+02 angle pdb=" C ASN C 339 " pdb=" N GLU C 340 " pdb=" CA GLU C 340 " ideal model delta sigma weight residual 121.54 136.88 -15.34 1.91e+00 2.74e-01 6.45e+01 angle pdb=" C ASN A 136 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.21e+01 angle pdb=" N HIS C 72 " pdb=" CA HIS C 72 " pdb=" C HIS C 72 " ideal model delta sigma weight residual 113.01 107.47 5.54 1.20e+00 6.94e-01 2.13e+01 angle pdb=" C2 NAG T 1 " pdb=" N2 NAG T 1 " pdb=" C7 NAG T 1 " ideal model delta sigma weight residual 124.56 138.18 -13.62 3.00e+00 1.11e-01 2.06e+01 ... (remaining 23739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10595 17.89 - 35.77: 890 35.77 - 53.66: 158 53.66 - 71.54: 59 71.54 - 89.43: 11 Dihedral angle restraints: 11713 sinusoidal: 5881 harmonic: 5832 Sorted by residual: dihedral pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 3.57 89.43 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual -86.00 -6.22 -79.78 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -155.80 69.80 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 11710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2739 0.101 - 0.203: 213 0.203 - 0.304: 9 0.304 - 0.405: 4 0.405 - 0.506: 2 Chirality restraints: 2967 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C2 NAG o 2 " pdb=" C1 NAG o 2 " pdb=" C3 NAG o 2 " pdb=" N2 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2964 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 83 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLU C 83 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU C 83 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE C 84 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C GLU C 340 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 341 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR G 140 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 141 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " 0.039 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4780 2.82 - 3.34: 13524 3.34 - 3.86: 26591 3.86 - 4.38: 28218 4.38 - 4.90: 52161 Nonbonded interactions: 125274 Sorted by model distance: nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR E 297 " pdb=" O7 NAG m 1 " model vdw 2.311 3.040 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR D 606 " model vdw 2.326 3.040 nonbonded pdb=" O LYS H 143 " pdb=" OG SER H 177 " model vdw 2.333 3.040 nonbonded pdb=" O THR C 337 " pdb=" OG1 THR C 341 " model vdw 2.343 3.040 ... (remaining 125269 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 34 through 56 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 133 or resid 142 thro \ ugh 177 or resid 188 through 398 or resid 412 through 604)) selection = (chain 'C' and (resid 34 through 56 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 398 or resid 412 through 458 or re \ sid 463 through 604)) selection = (chain 'E' and (resid 34 through 56 or resid 67 through 79 or (resid 80 and (nam \ e N or name CA or name C or name O or name CB )) or resid 81 through 133 or resi \ d 142 through 177 or resid 188 through 458 or resid 463 through 604)) } ncs_group { reference = (chain 'B' and (resid 519 through 547 or resid 572 through 701)) selection = (chain 'D' and (resid 519 through 547 or resid 572 through 701)) selection = (chain 'F' and (resid 519 through 547 or resid 572 through 701)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'c' selection = chain 'i' selection = chain 'n' selection = chain 'o' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.210 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.004 0.095 17612 Z= 0.204 Angle : 0.963 23.727 24087 Z= 0.460 Chirality : 0.055 0.506 2967 Planarity : 0.005 0.074 2892 Dihedral : 13.168 86.105 7850 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -2.02 (0.18), residues: 1970 helix: -1.29 (0.24), residues: 360 sheet: -0.53 (0.23), residues: 543 loop : -1.81 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 76 TYR 0.023 0.001 TYR G 140 PHE 0.028 0.002 PHE G 49 TRP 0.027 0.001 TRP C 112 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00406 (17488) covalent geometry : angle 0.89491 (23744) SS BOND : bond 0.01292 ( 29) SS BOND : angle 4.03138 ( 58) hydrogen bonds : bond 0.22180 ( 509) hydrogen bonds : angle 8.10913 ( 1473) link_BETA1-4 : bond 0.00654 ( 39) link_BETA1-4 : angle 2.24241 ( 117) link_NAG-ASN : bond 0.00676 ( 56) link_NAG-ASN : angle 3.26102 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7834 (mmm) cc_final: 0.7413 (mmt) REVERT: A 484 TYR cc_start: 0.9105 (p90) cc_final: 0.8491 (p90) REVERT: B 584 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 114 GLN cc_start: 0.8036 (tt0) cc_final: 0.7716 (mt0) REVERT: C 217 TYR cc_start: 0.8158 (m-80) cc_final: 0.7695 (m-80) REVERT: C 457 ASP cc_start: 0.7708 (t0) cc_final: 0.6954 (t0) REVERT: D 543 ASN cc_start: 0.8576 (t0) cc_final: 0.8201 (t0) REVERT: D 621 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 625 ASN cc_start: 0.8586 (t0) cc_final: 0.8233 (t0) REVERT: D 657 GLU cc_start: 0.8319 (tp30) cc_final: 0.8088 (tp30) REVERT: E 141 ASP cc_start: 0.8165 (m-30) cc_final: 0.7879 (m-30) REVERT: E 322 ILE cc_start: 0.8351 (mt) cc_final: 0.8117 (mm) REVERT: E 356 ASN cc_start: 0.8610 (t0) cc_final: 0.8292 (t0) REVERT: F 615 SER cc_start: 0.8325 (t) cc_final: 0.8090 (t) REVERT: G 167 GLN cc_start: 0.6116 (tt0) cc_final: 0.5269 (pm20) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.1301 time to fit residues: 45.7155 Evaluate side-chains 190 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 80 ASN A 99 ASN C 162 GLN C 216 HIS C 478 ASN D 640 GLN E 99 ASN E 105 HIS F 637 ASN G 108 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086649 restraints weight = 28795.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089501 restraints weight = 18631.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091386 restraints weight = 14211.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092649 restraints weight = 11900.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093371 restraints weight = 10568.742| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 17612 Z= 0.277 Angle : 0.784 17.664 24087 Z= 0.375 Chirality : 0.050 0.421 2967 Planarity : 0.004 0.052 2892 Dihedral : 7.959 59.886 4126 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.57 % Allowed : 7.95 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -1.63 (0.18), residues: 1970 helix: -0.21 (0.28), residues: 378 sheet: -0.54 (0.22), residues: 586 loop : -1.76 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 76 TYR 0.016 0.002 TYR H 50 PHE 0.025 0.002 PHE G 49 TRP 0.023 0.002 TRP C 112 HIS 0.006 0.002 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00657 (17488) covalent geometry : angle 0.71253 (23744) SS BOND : bond 0.01312 ( 29) SS BOND : angle 3.97352 ( 58) hydrogen bonds : bond 0.04828 ( 509) hydrogen bonds : angle 5.62299 ( 1473) link_BETA1-4 : bond 0.00416 ( 39) link_BETA1-4 : angle 2.07348 ( 117) link_NAG-ASN : bond 0.00632 ( 56) link_NAG-ASN : angle 2.81582 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.8443 (p90) cc_final: 0.8200 (p90) REVERT: A 475 MET cc_start: 0.8050 (mmm) cc_final: 0.7538 (mmp) REVERT: A 484 TYR cc_start: 0.9176 (p90) cc_final: 0.8585 (p90) REVERT: B 584 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 114 GLN cc_start: 0.8161 (tt0) cc_final: 0.7863 (mt0) REVERT: C 217 TYR cc_start: 0.8555 (m-80) cc_final: 0.8133 (m-80) REVERT: D 543 ASN cc_start: 0.8603 (t0) cc_final: 0.8258 (t0) REVERT: D 621 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8174 (tm-30) REVERT: D 625 ASN cc_start: 0.8629 (t0) cc_final: 0.8212 (t0) REVERT: D 657 GLU cc_start: 0.8368 (tp30) cc_final: 0.8086 (tp30) REVERT: E 141 ASP cc_start: 0.8189 (m-30) cc_final: 0.7871 (m-30) REVERT: E 153 MET cc_start: 0.8760 (tpt) cc_final: 0.8354 (tpp) REVERT: E 322 ILE cc_start: 0.8623 (mt) cc_final: 0.8350 (mm) REVERT: E 356 ASN cc_start: 0.8689 (t0) cc_final: 0.8358 (t0) REVERT: F 632 ASP cc_start: 0.8562 (t70) cc_final: 0.8269 (t0) REVERT: F 657 GLU cc_start: 0.8287 (tp30) cc_final: 0.8054 (tm-30) REVERT: G 138 ASP cc_start: 0.7277 (t70) cc_final: 0.7075 (t70) REVERT: G 167 GLN cc_start: 0.6065 (tt0) cc_final: 0.5294 (pm20) REVERT: H 35 SER cc_start: 0.9116 (t) cc_final: 0.8913 (t) outliers start: 28 outliers final: 20 residues processed: 211 average time/residue: 0.1298 time to fit residues: 41.2422 Evaluate side-chains 201 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 96 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN E 99 ASN F 540 GLN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.088842 restraints weight = 28635.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091708 restraints weight = 18631.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093587 restraints weight = 14173.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094842 restraints weight = 11860.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095600 restraints weight = 10527.495| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17612 Z= 0.127 Angle : 0.660 13.648 24087 Z= 0.308 Chirality : 0.046 0.393 2967 Planarity : 0.003 0.051 2892 Dihedral : 7.529 59.735 4126 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 1.62 % Allowed : 10.08 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -1.24 (0.19), residues: 1970 helix: 0.50 (0.29), residues: 365 sheet: -0.32 (0.22), residues: 579 loop : -1.65 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 76 TYR 0.024 0.001 TYR C 484 PHE 0.020 0.001 PHE G 49 TRP 0.014 0.001 TRP C 112 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00294 (17488) covalent geometry : angle 0.59062 (23744) SS BOND : bond 0.00919 ( 29) SS BOND : angle 3.39543 ( 58) hydrogen bonds : bond 0.03841 ( 509) hydrogen bonds : angle 5.14340 ( 1473) link_BETA1-4 : bond 0.00440 ( 39) link_BETA1-4 : angle 1.90550 ( 117) link_NAG-ASN : bond 0.00489 ( 56) link_NAG-ASN : angle 2.56014 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7929 (mmm) cc_final: 0.7426 (mmp) REVERT: A 484 TYR cc_start: 0.9183 (p90) cc_final: 0.8661 (p90) REVERT: B 542 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.8042 (mtm-85) REVERT: B 545 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 584 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 49 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 114 GLN cc_start: 0.8152 (tt0) cc_final: 0.7835 (mt0) REVERT: C 125 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (tt) REVERT: C 217 TYR cc_start: 0.8506 (m-80) cc_final: 0.8123 (m-80) REVERT: D 543 ASN cc_start: 0.8610 (t0) cc_final: 0.8248 (t0) REVERT: D 625 ASN cc_start: 0.8641 (t0) cc_final: 0.8235 (t0) REVERT: D 657 GLU cc_start: 0.8318 (tp30) cc_final: 0.7992 (tp30) REVERT: E 356 ASN cc_start: 0.8641 (t0) cc_final: 0.8243 (t0) REVERT: F 615 SER cc_start: 0.8393 (t) cc_final: 0.8091 (t) REVERT: F 632 ASP cc_start: 0.8559 (t70) cc_final: 0.8300 (t0) REVERT: F 657 GLU cc_start: 0.8282 (tp30) cc_final: 0.8080 (tm-30) REVERT: G 138 ASP cc_start: 0.7265 (t70) cc_final: 0.7028 (t70) outliers start: 29 outliers final: 18 residues processed: 214 average time/residue: 0.1292 time to fit residues: 41.2570 Evaluate side-chains 210 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 194 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN F 650 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085879 restraints weight = 28950.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.088579 restraints weight = 18991.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090393 restraints weight = 14667.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091575 restraints weight = 12368.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092270 restraints weight = 11056.901| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17612 Z= 0.221 Angle : 0.699 13.426 24087 Z= 0.330 Chirality : 0.048 0.379 2967 Planarity : 0.004 0.047 2892 Dihedral : 7.695 59.515 4126 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 2.30 % Allowed : 11.42 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.19), residues: 1970 helix: 0.56 (0.29), residues: 365 sheet: -0.41 (0.22), residues: 582 loop : -1.68 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.023 0.002 TYR C 484 PHE 0.020 0.002 PHE G 49 TRP 0.015 0.001 TRP C 112 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00529 (17488) covalent geometry : angle 0.63853 (23744) SS BOND : bond 0.01168 ( 29) SS BOND : angle 2.87598 ( 58) hydrogen bonds : bond 0.04152 ( 509) hydrogen bonds : angle 5.03082 ( 1473) link_BETA1-4 : bond 0.00391 ( 39) link_BETA1-4 : angle 1.93180 ( 117) link_NAG-ASN : bond 0.00501 ( 56) link_NAG-ASN : angle 2.63329 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8096 (mmm) cc_final: 0.7592 (mmp) REVERT: A 484 TYR cc_start: 0.9269 (p90) cc_final: 0.8673 (p90) REVERT: B 545 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 584 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8093 (tm-30) REVERT: C 49 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: C 114 GLN cc_start: 0.8195 (tt0) cc_final: 0.7849 (tm-30) REVERT: C 125 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8341 (tt) REVERT: C 217 TYR cc_start: 0.8681 (m-80) cc_final: 0.8365 (m-80) REVERT: D 543 ASN cc_start: 0.8661 (t0) cc_final: 0.8300 (t0) REVERT: D 584 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7333 (tm-30) REVERT: D 621 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8476 (tm-30) REVERT: D 625 ASN cc_start: 0.8637 (t0) cc_final: 0.8199 (t0) REVERT: E 356 ASN cc_start: 0.8696 (t0) cc_final: 0.8316 (t0) REVERT: F 657 GLU cc_start: 0.8268 (tp30) cc_final: 0.8057 (tm-30) REVERT: G 194 GLN cc_start: 0.5427 (mm-40) cc_final: 0.5148 (mp10) outliers start: 41 outliers final: 29 residues processed: 217 average time/residue: 0.1261 time to fit residues: 40.9134 Evaluate side-chains 209 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 189 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087843 restraints weight = 28471.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090525 restraints weight = 18886.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092307 restraints weight = 14643.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093322 restraints weight = 12400.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094231 restraints weight = 11146.142| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17612 Z= 0.149 Angle : 0.647 12.916 24087 Z= 0.303 Chirality : 0.046 0.369 2967 Planarity : 0.003 0.047 2892 Dihedral : 7.491 59.467 4126 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 2.74 % Allowed : 11.87 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1970 helix: 0.83 (0.29), residues: 363 sheet: -0.31 (0.22), residues: 579 loop : -1.64 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.021 0.001 TYR C 484 PHE 0.019 0.001 PHE G 49 TRP 0.012 0.001 TRP C 112 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00355 (17488) covalent geometry : angle 0.58735 (23744) SS BOND : bond 0.00954 ( 29) SS BOND : angle 2.80492 ( 58) hydrogen bonds : bond 0.03663 ( 509) hydrogen bonds : angle 4.82124 ( 1473) link_BETA1-4 : bond 0.00411 ( 39) link_BETA1-4 : angle 1.83659 ( 117) link_NAG-ASN : bond 0.00443 ( 56) link_NAG-ASN : angle 2.49958 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7720 (tpt) cc_final: 0.7506 (mmt) REVERT: A 475 MET cc_start: 0.8026 (mmm) cc_final: 0.7533 (mmp) REVERT: A 484 TYR cc_start: 0.9222 (p90) cc_final: 0.8670 (p90) REVERT: B 544 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9005 (mm) REVERT: B 584 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 588 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7572 (ttm-80) REVERT: C 49 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: C 114 GLN cc_start: 0.8184 (tt0) cc_final: 0.7862 (tm-30) REVERT: C 125 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8287 (tt) REVERT: C 217 TYR cc_start: 0.8701 (m-80) cc_final: 0.8396 (m-80) REVERT: D 543 ASN cc_start: 0.8632 (t0) cc_final: 0.8257 (t0) REVERT: D 621 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8458 (tm-30) REVERT: D 625 ASN cc_start: 0.8618 (t0) cc_final: 0.8211 (t0) REVERT: E 356 ASN cc_start: 0.8643 (t0) cc_final: 0.8293 (t0) REVERT: G 194 GLN cc_start: 0.5446 (mm-40) cc_final: 0.5207 (mp10) REVERT: H 75 GLU cc_start: 0.8243 (pt0) cc_final: 0.7526 (pt0) outliers start: 49 outliers final: 34 residues processed: 218 average time/residue: 0.1265 time to fit residues: 41.7031 Evaluate side-chains 216 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 171 optimal weight: 0.1980 chunk 75 optimal weight: 0.4980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS D 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089654 restraints weight = 28380.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092393 restraints weight = 18778.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094257 restraints weight = 14484.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095456 restraints weight = 12204.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096292 restraints weight = 10897.734| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17612 Z= 0.104 Angle : 0.610 11.431 24087 Z= 0.285 Chirality : 0.045 0.367 2967 Planarity : 0.003 0.046 2892 Dihedral : 7.172 59.996 4126 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 2.18 % Allowed : 12.88 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 1970 helix: 1.14 (0.30), residues: 363 sheet: -0.23 (0.22), residues: 567 loop : -1.52 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.016 0.001 TYR C 484 PHE 0.017 0.001 PHE G 49 TRP 0.010 0.001 TRP A 69 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00238 (17488) covalent geometry : angle 0.55502 (23744) SS BOND : bond 0.00643 ( 29) SS BOND : angle 2.42172 ( 58) hydrogen bonds : bond 0.03180 ( 509) hydrogen bonds : angle 4.57656 ( 1473) link_BETA1-4 : bond 0.00443 ( 39) link_BETA1-4 : angle 1.75365 ( 117) link_NAG-ASN : bond 0.00445 ( 56) link_NAG-ASN : angle 2.38694 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7620 (tpt) cc_final: 0.7323 (mmt) REVERT: A 475 MET cc_start: 0.7966 (mmm) cc_final: 0.7465 (mmp) REVERT: A 484 TYR cc_start: 0.9224 (p90) cc_final: 0.8723 (p90) REVERT: B 530 MET cc_start: 0.8727 (mtt) cc_final: 0.8384 (mtp) REVERT: B 584 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 588 ARG cc_start: 0.7866 (tpt170) cc_final: 0.7543 (ttm-80) REVERT: C 49 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 114 GLN cc_start: 0.8164 (tt0) cc_final: 0.7901 (tm-30) REVERT: C 125 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 217 TYR cc_start: 0.8690 (m-80) cc_final: 0.8336 (m-80) REVERT: D 543 ASN cc_start: 0.8650 (t0) cc_final: 0.8237 (t0) REVERT: D 621 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 625 ASN cc_start: 0.8613 (t0) cc_final: 0.8256 (t0) REVERT: E 356 ASN cc_start: 0.8616 (t0) cc_final: 0.8262 (t0) REVERT: F 543 ASN cc_start: 0.8693 (m-40) cc_final: 0.8374 (m110) REVERT: F 657 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8337 (tp30) REVERT: G 194 GLN cc_start: 0.5523 (mm-40) cc_final: 0.5276 (mp10) REVERT: H 72 ASP cc_start: 0.7637 (t0) cc_final: 0.7093 (t0) outliers start: 39 outliers final: 25 residues processed: 216 average time/residue: 0.1283 time to fit residues: 41.4958 Evaluate side-chains 209 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089151 restraints weight = 28392.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.091898 restraints weight = 18701.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093737 restraints weight = 14399.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094951 restraints weight = 12121.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095758 restraints weight = 10793.972| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17612 Z= 0.113 Angle : 0.612 10.710 24087 Z= 0.286 Chirality : 0.045 0.362 2967 Planarity : 0.003 0.045 2892 Dihedral : 7.034 59.532 4126 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.41 % Allowed : 13.38 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.19), residues: 1970 helix: 1.28 (0.30), residues: 363 sheet: -0.20 (0.22), residues: 582 loop : -1.46 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.027 0.001 TYR C 484 PHE 0.016 0.001 PHE G 49 TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00264 (17488) covalent geometry : angle 0.55476 (23744) SS BOND : bond 0.00725 ( 29) SS BOND : angle 2.73262 ( 58) hydrogen bonds : bond 0.03160 ( 509) hydrogen bonds : angle 4.45120 ( 1473) link_BETA1-4 : bond 0.00434 ( 39) link_BETA1-4 : angle 1.71920 ( 117) link_NAG-ASN : bond 0.00429 ( 56) link_NAG-ASN : angle 2.34736 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7993 (mmm) cc_final: 0.7491 (mmp) REVERT: A 484 TYR cc_start: 0.9231 (p90) cc_final: 0.8734 (p90) REVERT: B 530 MET cc_start: 0.8701 (mtt) cc_final: 0.8376 (mtp) REVERT: B 584 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 588 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7549 (ttm-80) REVERT: C 49 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: C 114 GLN cc_start: 0.8160 (tt0) cc_final: 0.7903 (tm-30) REVERT: C 125 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8346 (tt) REVERT: C 217 TYR cc_start: 0.8724 (m-80) cc_final: 0.8397 (m-80) REVERT: D 543 ASN cc_start: 0.8654 (t0) cc_final: 0.8239 (t0) REVERT: D 621 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8506 (tm-30) REVERT: D 625 ASN cc_start: 0.8659 (t0) cc_final: 0.8305 (t0) REVERT: E 356 ASN cc_start: 0.8590 (t0) cc_final: 0.8225 (t0) REVERT: F 657 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8402 (tp30) REVERT: G 194 GLN cc_start: 0.5639 (mm-40) cc_final: 0.5427 (mp10) outliers start: 43 outliers final: 31 residues processed: 216 average time/residue: 0.1253 time to fit residues: 40.7746 Evaluate side-chains 216 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 171 optimal weight: 0.0570 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 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 = 0.3461 r_free = 0.3461 target = 0.117008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.088663 restraints weight = 28628.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091447 restraints weight = 18829.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093269 restraints weight = 14431.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094476 restraints weight = 12157.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095223 restraints weight = 10840.552| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17612 Z= 0.125 Angle : 0.626 13.395 24087 Z= 0.293 Chirality : 0.046 0.359 2967 Planarity : 0.003 0.045 2892 Dihedral : 7.015 59.498 4126 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 2.18 % Allowed : 13.44 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 1970 helix: 1.37 (0.30), residues: 357 sheet: -0.18 (0.22), residues: 586 loop : -1.47 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.016 0.001 TYR C 484 PHE 0.016 0.001 PHE G 49 TRP 0.011 0.001 TRP A 69 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00294 (17488) covalent geometry : angle 0.56420 (23744) SS BOND : bond 0.00976 ( 29) SS BOND : angle 3.26174 ( 58) hydrogen bonds : bond 0.03200 ( 509) hydrogen bonds : angle 4.42179 ( 1473) link_BETA1-4 : bond 0.00424 ( 39) link_BETA1-4 : angle 1.67744 ( 117) link_NAG-ASN : bond 0.00408 ( 56) link_NAG-ASN : angle 2.35412 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8014 (mmm) cc_final: 0.7529 (mmp) REVERT: A 484 TYR cc_start: 0.9231 (p90) cc_final: 0.8726 (p90) REVERT: B 584 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 588 ARG cc_start: 0.7862 (tpt170) cc_final: 0.7543 (ttm-80) REVERT: C 49 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: C 114 GLN cc_start: 0.8136 (tt0) cc_final: 0.7895 (tm-30) REVERT: C 125 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (tt) REVERT: C 217 TYR cc_start: 0.8739 (m-80) cc_final: 0.8425 (m-80) REVERT: D 543 ASN cc_start: 0.8667 (t0) cc_final: 0.8253 (t0) REVERT: D 621 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 625 ASN cc_start: 0.8639 (t0) cc_final: 0.8283 (t0) REVERT: E 356 ASN cc_start: 0.8583 (t0) cc_final: 0.8223 (t0) REVERT: F 543 ASN cc_start: 0.8599 (m-40) cc_final: 0.8323 (m110) REVERT: G 194 GLN cc_start: 0.5800 (mm-40) cc_final: 0.5550 (mp10) REVERT: H 56 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7411 (mt-10) outliers start: 39 outliers final: 31 residues processed: 214 average time/residue: 0.1254 time to fit residues: 40.4383 Evaluate side-chains 214 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 30 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 0.0050 chunk 93 optimal weight: 6.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN D 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091208 restraints weight = 28488.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093728 restraints weight = 20199.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095149 restraints weight = 15261.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095361 restraints weight = 13354.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095534 restraints weight = 12683.170| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17612 Z= 0.098 Angle : 0.612 13.885 24087 Z= 0.287 Chirality : 0.045 0.351 2967 Planarity : 0.003 0.045 2892 Dihedral : 6.852 59.905 4126 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 2.13 % Allowed : 13.77 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1970 helix: 1.41 (0.30), residues: 363 sheet: -0.10 (0.22), residues: 586 loop : -1.38 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 76 TYR 0.026 0.001 TYR C 484 PHE 0.015 0.001 PHE G 49 TRP 0.012 0.001 TRP A 69 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00220 (17488) covalent geometry : angle 0.54873 (23744) SS BOND : bond 0.00945 ( 29) SS BOND : angle 3.60861 ( 58) hydrogen bonds : bond 0.02870 ( 509) hydrogen bonds : angle 4.29351 ( 1473) link_BETA1-4 : bond 0.00461 ( 39) link_BETA1-4 : angle 1.64518 ( 117) link_NAG-ASN : bond 0.00428 ( 56) link_NAG-ASN : angle 2.20195 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7958 (mmm) cc_final: 0.7476 (mmp) REVERT: A 484 TYR cc_start: 0.9205 (p90) cc_final: 0.8451 (p90) REVERT: B 584 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 588 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7543 (ttm-80) REVERT: C 49 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: C 114 GLN cc_start: 0.8134 (tt0) cc_final: 0.7893 (tm-30) REVERT: C 217 TYR cc_start: 0.8723 (m-80) cc_final: 0.8434 (m-80) REVERT: D 543 ASN cc_start: 0.8639 (t0) cc_final: 0.8229 (t0) REVERT: D 621 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8290 (tm-30) REVERT: D 625 ASN cc_start: 0.8645 (t0) cc_final: 0.8343 (t0) REVERT: E 356 ASN cc_start: 0.8547 (t0) cc_final: 0.8224 (t0) REVERT: F 543 ASN cc_start: 0.8519 (m-40) cc_final: 0.8253 (m110) REVERT: G 194 GLN cc_start: 0.5851 (mm-40) cc_final: 0.5629 (mp10) outliers start: 38 outliers final: 28 residues processed: 219 average time/residue: 0.1319 time to fit residues: 43.4859 Evaluate side-chains 214 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 181 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087534 restraints weight = 28225.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090439 restraints weight = 18039.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092367 restraints weight = 13620.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093469 restraints weight = 11356.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094363 restraints weight = 10151.729| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17612 Z= 0.184 Angle : 0.679 15.178 24087 Z= 0.319 Chirality : 0.047 0.351 2967 Planarity : 0.003 0.044 2892 Dihedral : 7.115 59.994 4126 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.90 % Allowed : 13.72 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.19), residues: 1970 helix: 1.39 (0.30), residues: 357 sheet: -0.15 (0.22), residues: 593 loop : -1.48 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.025 0.001 TYR C 484 PHE 0.026 0.002 PHE G 49 TRP 0.013 0.001 TRP A 69 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00444 (17488) covalent geometry : angle 0.61826 (23744) SS BOND : bond 0.01194 ( 29) SS BOND : angle 3.58117 ( 58) hydrogen bonds : bond 0.03524 ( 509) hydrogen bonds : angle 4.47177 ( 1473) link_BETA1-4 : bond 0.00385 ( 39) link_BETA1-4 : angle 1.69445 ( 117) link_NAG-ASN : bond 0.00425 ( 56) link_NAG-ASN : angle 2.36531 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7990 (mmm) cc_final: 0.7498 (mmp) REVERT: A 484 TYR cc_start: 0.9270 (p90) cc_final: 0.8716 (p90) REVERT: B 545 LEU cc_start: 0.8906 (mt) cc_final: 0.8587 (mt) REVERT: B 584 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 588 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7548 (ttm-80) REVERT: C 49 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: C 114 GLN cc_start: 0.8131 (tt0) cc_final: 0.7864 (tm-30) REVERT: C 217 TYR cc_start: 0.8762 (m-80) cc_final: 0.8452 (m-80) REVERT: D 543 ASN cc_start: 0.8699 (t0) cc_final: 0.8268 (t0) REVERT: D 621 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8447 (tm-30) REVERT: D 625 ASN cc_start: 0.8658 (t0) cc_final: 0.8289 (t0) REVERT: E 356 ASN cc_start: 0.8592 (t0) cc_final: 0.8267 (t0) REVERT: G 194 GLN cc_start: 0.5827 (mm-40) cc_final: 0.5573 (mp10) outliers start: 34 outliers final: 32 residues processed: 210 average time/residue: 0.1273 time to fit residues: 40.1708 Evaluate side-chains 214 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 153 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** D 540 GLN ** 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 = 0.3471 r_free = 0.3471 target = 0.117739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090182 restraints weight = 28197.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093015 restraints weight = 18190.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094851 restraints weight = 13740.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096092 restraints weight = 11495.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096821 restraints weight = 10168.597| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17612 Z= 0.110 Angle : 0.633 13.892 24087 Z= 0.295 Chirality : 0.045 0.344 2967 Planarity : 0.003 0.044 2892 Dihedral : 6.955 59.620 4126 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.74 % Allowed : 14.39 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.19), residues: 1970 helix: 1.46 (0.30), residues: 358 sheet: 0.05 (0.23), residues: 575 loop : -1.45 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 542 TYR 0.025 0.001 TYR C 484 PHE 0.024 0.001 PHE G 49 TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00257 (17488) covalent geometry : angle 0.57501 (23744) SS BOND : bond 0.00961 ( 29) SS BOND : angle 3.33966 ( 58) hydrogen bonds : bond 0.03060 ( 509) hydrogen bonds : angle 4.34835 ( 1473) link_BETA1-4 : bond 0.00439 ( 39) link_BETA1-4 : angle 1.63676 ( 117) link_NAG-ASN : bond 0.00407 ( 56) link_NAG-ASN : angle 2.22985 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.22 seconds wall clock time: 45 minutes 11.37 seconds (2711.37 seconds total)