Starting phenix.real_space_refine on Fri Jun 20 14:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehm_48060/06_2025/9ehm_48060.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.001 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 142 5.16 5 C 14964 2.51 5 N 4044 2.21 5 O 4793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23943 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3458 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3478 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 4 Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3462 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 418} Chain breaks: 4 Chain: "D" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 999 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "I" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "N" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "O" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "R" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} 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: "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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 3, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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 Time building chain proxies: 14.70, per 1000 atoms: 0.61 Number of scatterers: 23943 At special positions: 0 Unit cell: (160.576, 142.272, 153.088, 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 142 16.00 O 4793 8.00 N 4044 7.00 C 14964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.05 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-4 " NAG T 2 " - " MAN T 3 " " NAG a 2 " - " MAN a 3 " " NAG g 2 " - " MAN g 3 " " NAG k 2 " - " MAN k 3 " BETA1-2 " MAN o 4 " - " BMA o 5 " BETA1-3 " MAN T 3 " - " BMA T 4 " " BMA W 3 " - " BMA W 4 " " MAN a 3 " - " BMA a 4 " " BMA j 3 " - " BMA j 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 " BETA1-6 " BMA o 3 " - " BMA o 6 " NAG-ASN " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 363 " " NAG B 601 " - " ASN B 339 " " NAG B 602 " - " ASN B 88 " " NAG B 603 " - " ASN B 234 " " NAG B 604 " - " ASN B 295 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 448 " " NAG B 607 " - " ASN B 133 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN B 156 " " NAG Y 1 " - " ASN B 160 " " NAG Z 1 " - " ASN B 197 " " NAG a 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 276 " " NAG c 1 " - " ASN B 301 " " NAG d 1 " - " ASN B 332 " " NAG e 1 " - " ASN B 386 " " NAG f 1 " - " ASN B 363 " " NAG g 1 " - " ASN C 156 " " NAG h 1 " - " ASN C 160 " " NAG i 1 " - " ASN C 197 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 301 " " NAG m 1 " - " ASN C 363 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 332 " Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5328 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 54 sheets defined 18.2% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.371A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.707A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.679A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.921A pdb=" N ALA B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.668A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.950A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.625A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.599A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.263A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.751A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.509A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.754A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 663 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.023A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.516A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.016A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 664 removed outlier: 3.641A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.213A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.524A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 634 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.048A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 664 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.900A pdb=" N GLY H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.661A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100C through 100G Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.789A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100G Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.579A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.078A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 64 removed outlier: 3.610A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.595A pdb=" N ASN O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.911A pdb=" N THR O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 100D through 100H removed outlier: 3.532A pdb=" N PHE O 100G" --> pdb=" O VAL O 100D" (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.993A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 4.182A pdb=" N GLU Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.759A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.957A pdb=" N ASN A 67 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.575A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.643A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.464A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.404A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.779A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 40 Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.231A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.774A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 93 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 176 Processing sheet with id=AB7, first strand: chain 'B' and resid 200 through 203 removed outlier: 5.657A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.569A pdb=" N LEU B 454 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 287 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 271 " --> pdb=" O GLN B 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.359A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 374 through 377 removed outlier: 3.523A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 296 " --> pdb=" O CYS B 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.159A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.744A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AC7, first strand: chain 'C' and resid 169 through 176 removed outlier: 4.302A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 374 through 377 removed outlier: 3.664A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.887A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD4, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.143A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.657A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.245A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.765A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AE4, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.728A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU M 80 " --> pdb=" O VAL M 20 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 45 through 51 removed outlier: 6.732A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR M 33 " --> pdb=" O ALA M 95 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'N' and resid 45 through 51 removed outlier: 6.926A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR N 33 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE N 37 " --> pdb=" O TYR N 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 45 through 51 removed outlier: 6.926A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR N 33 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE N 37 " --> pdb=" O TYR N 91 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR N 107 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.550A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR O 33 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE O 51 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP O 36 " --> pdb=" O GLY O 49 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.550A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 68 through 72 Processing sheet with id=AF4, first strand: chain 'P' and resid 9 through 11 removed outlier: 5.763A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'Q' and resid 9 through 14 removed outlier: 5.688A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR Q 105 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU Q 107 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 18 through 22 removed outlier: 3.502A pdb=" N THR Q 74 " --> pdb=" O SER Q 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 19 through 22 Processing sheet with id=AF9, first strand: chain 'R' and resid 32 through 38 removed outlier: 3.658A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 1980 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: 9.04 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 3782 1.26 - 1.40: 5867 1.40 - 1.55: 14579 1.55 - 1.70: 11 1.70 - 1.84: 198 Bond restraints: 24437 Sorted by residual: bond pdb=" C GLY L 94 " pdb=" N VAL L 96 " ideal model delta sigma weight residual 1.334 1.111 0.223 1.26e-02 6.30e+03 3.13e+02 bond pdb=" N ILE F 635 " pdb=" CA ILE F 635 " ideal model delta sigma weight residual 1.459 1.498 -0.039 9.10e-03 1.21e+04 1.88e+01 bond pdb=" N PRO K 55 " pdb=" CD PRO K 55 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" CA ARG K 54 " pdb=" C ARG K 54 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N ASN A 392 " pdb=" CA ASN A 392 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.24e+01 ... (remaining 24432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 32242 2.52 - 5.03: 854 5.03 - 7.55: 64 7.55 - 10.07: 11 10.07 - 12.58: 4 Bond angle restraints: 33175 Sorted by residual: angle pdb=" O LYS K 53 " pdb=" C LYS K 53 " pdb=" N ARG K 54 " ideal model delta sigma weight residual 123.22 111.77 11.45 1.14e+00 7.69e-01 1.01e+02 angle pdb=" O GLY L 94 " pdb=" C GLY L 94 " pdb=" N VAL L 96 " ideal model delta sigma weight residual 122.70 133.77 -11.07 1.30e+00 5.92e-01 7.25e+01 angle pdb=" N ILE Q 66B" pdb=" CA ILE Q 66B" pdb=" C ILE Q 66B" ideal model delta sigma weight residual 111.88 104.89 6.99 1.06e+00 8.90e-01 4.34e+01 angle pdb=" N ILE R 66B" pdb=" CA ILE R 66B" pdb=" C ILE R 66B" ideal model delta sigma weight residual 111.88 105.38 6.50 1.06e+00 8.90e-01 3.76e+01 angle pdb=" CA ARG K 54 " pdb=" C ARG K 54 " pdb=" N PRO K 55 " ideal model delta sigma weight residual 118.81 126.59 -7.78 1.29e+00 6.01e-01 3.64e+01 ... (remaining 33170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 14641 23.29 - 46.58: 794 46.58 - 69.87: 176 69.87 - 93.16: 90 93.16 - 116.45: 150 Dihedral angle restraints: 15851 sinusoidal: 7547 harmonic: 8304 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 3.12 -89.12 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 1.80 -87.80 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual -86.00 -2.17 -83.83 1 1.00e+01 1.00e-02 8.57e+01 ... (remaining 15848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.995: 3960 0.995 - 1.989: 1 1.989 - 2.984: 0 2.984 - 3.979: 0 3.979 - 4.974: 3 Chirality restraints: 3964 Sorted by residual: chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 2.35 -4.75 2.00e-02 2.50e+03 5.63e+04 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.09e+03 chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 2.57 -4.97 2.00e-01 2.50e+01 6.18e+02 ... (remaining 3961 not shown) Planarity restraints: 4160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.102 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" CG ASN C 448 " -0.095 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.532 2.00e-02 2.50e+03 pdb=" C1 NAG C 607 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " -0.110 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" CG ASN C 386 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " -0.160 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " 0.534 2.00e-02 2.50e+03 pdb=" C1 NAG n 1 " -0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 605 " 0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A 605 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 605 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG A 605 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A 605 " 0.144 2.00e-02 2.50e+03 ... (remaining 4157 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 4 2.13 - 2.82: 7163 2.82 - 3.51: 33676 3.51 - 4.21: 57906 4.21 - 4.90: 95920 Nonbonded interactions: 194669 Sorted by model distance: nonbonded pdb=" OG SER C 388 " pdb=" C1 NAG n 1 " model vdw 1.433 3.470 nonbonded pdb=" OE1 GLN B 258 " pdb=" OG1 THR B 387 " model vdw 1.874 3.040 nonbonded pdb=" NE2 GLN B 258 " pdb=" O THR B 372 " model vdw 1.878 3.120 nonbonded pdb=" NE ARG A 503 " pdb=" O CYS D 605 " model vdw 2.094 3.120 nonbonded pdb=" OD1 ASP L 27B" pdb=" OG SER L 90 " model vdw 2.128 3.040 ... (remaining 194664 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 36 through 185 or resid 189 through 458 or resid 464 throu \ gh 505 or resid 601 through 607)) selection = (chain 'B' and (resid 36 through 58 or resid 63 through 136 or resid 152 through \ 185 or resid 189 through 505 or resid 601 through 607)) selection = (chain 'C' and (resid 36 through 58 or resid 63 through 136 or resid 152 through \ 458 or resid 464 through 505 or resid 601 through 607)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 115) } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'T' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = chain 'g' selection = chain 'k' } 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: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 54.750 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.170 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.007 0.223 24580 Z= 0.425 Angle : 1.037 18.046 33560 Z= 0.557 Chirality : 0.148 4.974 3964 Planarity : 0.015 0.315 4106 Dihedral : 19.586 116.446 10391 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.72 % Allowed : 1.84 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.15), residues: 2836 helix: -0.88 (0.26), residues: 394 sheet: -1.15 (0.18), residues: 817 loop : -1.88 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP O 47 HIS 0.007 0.001 HIS C 374 PHE 0.034 0.001 PHE D 522 TYR 0.024 0.001 TYR F 586 ARG 0.007 0.001 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 54) link_NAG-ASN : angle 3.28079 ( 162) link_ALPHA1-4 : bond 0.04568 ( 4) link_ALPHA1-4 : angle 8.27122 ( 12) link_BETA1-2 : bond 0.04519 ( 1) link_BETA1-2 : angle 6.26675 ( 3) link_BETA1-4 : bond 0.04586 ( 31) link_BETA1-4 : angle 7.20583 ( 93) link_ALPHA1-3 : bond 0.04499 ( 4) link_ALPHA1-3 : angle 6.30421 ( 12) hydrogen bonds : bond 0.25208 ( 728) hydrogen bonds : angle 10.65596 ( 1980) link_BETA1-6 : bond 0.03794 ( 1) link_BETA1-6 : angle 3.53812 ( 3) SS BOND : bond 0.00491 ( 44) SS BOND : angle 2.45358 ( 88) link_BETA1-3 : bond 0.04538 ( 4) link_BETA1-3 : angle 4.80993 ( 12) covalent geometry : bond 0.00641 (24437) covalent geometry : angle 0.90660 (33175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 451 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6786 (mp0) REVERT: A 217 TYR cc_start: 0.6796 (m-10) cc_final: 0.6594 (m-10) REVERT: A 318 TYR cc_start: 0.8388 (m-80) cc_final: 0.8145 (m-80) REVERT: A 390 LEU cc_start: 0.9265 (mt) cc_final: 0.8915 (mt) REVERT: A 396 ILE cc_start: 0.7951 (pt) cc_final: 0.7515 (mm) REVERT: B 69 TRP cc_start: 0.5475 (t60) cc_final: 0.3063 (t60) REVERT: B 161 MET cc_start: 0.8246 (tpp) cc_final: 0.7843 (tpt) REVERT: B 175 LEU cc_start: 0.8935 (mt) cc_final: 0.8610 (mp) REVERT: B 359 ILE cc_start: 0.8454 (mt) cc_final: 0.8224 (mm) REVERT: B 434 MET cc_start: 0.8871 (ttp) cc_final: 0.8400 (ttp) REVERT: B 481 SER cc_start: 0.8939 (m) cc_final: 0.8301 (t) REVERT: B 492 GLU cc_start: 0.8372 (mp0) cc_final: 0.7929 (mm-30) REVERT: C 104 MET cc_start: 0.7770 (ttp) cc_final: 0.7001 (ttp) REVERT: C 434 MET cc_start: 0.8498 (tmm) cc_final: 0.7912 (ttt) REVERT: D 601 LYS cc_start: 0.7474 (pttm) cc_final: 0.7058 (ptpp) REVERT: D 602 LEU cc_start: 0.7680 (mp) cc_final: 0.7371 (tt) REVERT: E 596 TRP cc_start: 0.8473 (m-10) cc_final: 0.8161 (m-10) REVERT: F 595 ILE cc_start: 0.8627 (tp) cc_final: 0.8281 (tp) REVERT: F 634 GLU cc_start: 0.7108 (pt0) cc_final: 0.6868 (pt0) REVERT: F 640 GLN cc_start: 0.8733 (tp40) cc_final: 0.8147 (pm20) REVERT: F 650 GLN cc_start: 0.8066 (mm110) cc_final: 0.7783 (mm-40) REVERT: H 73 THR cc_start: 0.8715 (m) cc_final: 0.8209 (m) REVERT: H 76 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7774 (mp0) REVERT: H 77 ILE cc_start: 0.8843 (mm) cc_final: 0.8632 (mm) REVERT: I 47 TRP cc_start: 0.8251 (t60) cc_final: 0.7887 (t60) REVERT: I 80 MET cc_start: 0.8499 (tmm) cc_final: 0.6053 (tmm) REVERT: K 27 VAL cc_start: 0.6990 (t) cc_final: 0.6790 (m) REVERT: K 36 TYR cc_start: 0.7907 (m-80) cc_final: 0.7641 (m-80) REVERT: K 49 TYR cc_start: 0.7253 (p90) cc_final: 0.6401 (p90) REVERT: L 49 TYR cc_start: 0.5846 (t80) cc_final: 0.5133 (t80) REVERT: L 86 TYR cc_start: 0.7864 (m-80) cc_final: 0.7473 (m-80) REVERT: L 96 VAL cc_start: 0.7206 (t) cc_final: 0.6690 (t) REVERT: M 51 ILE cc_start: 0.7707 (mt) cc_final: 0.6995 (tp) REVERT: M 72 ASP cc_start: 0.7103 (p0) cc_final: 0.6516 (p0) REVERT: N 46 GLU cc_start: 0.7871 (tt0) cc_final: 0.7607 (tt0) REVERT: N 100 TYR cc_start: 0.7670 (p90) cc_final: 0.7212 (p90) REVERT: O 5 GLN cc_start: 0.8981 (mm110) cc_final: 0.8771 (mt0) REVERT: O 47 TRP cc_start: 0.5606 (p90) cc_final: 0.5346 (p90) REVERT: O 78 LEU cc_start: 0.6483 (mm) cc_final: 0.6122 (tp) REVERT: O 90 TYR cc_start: 0.8162 (m-10) cc_final: 0.7785 (m-80) REVERT: O 91 TYR cc_start: 0.6920 (m-10) cc_final: 0.6555 (m-80) REVERT: O 100 GLU cc_start: 0.6273 (tt0) cc_final: 0.5950 (tt0) REVERT: P 39 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7773 (ptt-90) REVERT: P 46 LEU cc_start: 0.8047 (pt) cc_final: 0.7459 (tt) REVERT: P 66 ILE cc_start: 0.7557 (mm) cc_final: 0.7120 (mp) REVERT: Q 90 MET cc_start: 0.8410 (ttp) cc_final: 0.8138 (ttp) REVERT: Q 95 SER cc_start: 0.7666 (t) cc_final: 0.7392 (t) REVERT: Q 96 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6210 (t-100) REVERT: Q 98 PHE cc_start: 0.6610 (m-80) cc_final: 0.6374 (m-80) REVERT: R 66 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7596 (Cg_endo) REVERT: R 90 MET cc_start: 0.7375 (tmm) cc_final: 0.6892 (tmm) outliers start: 18 outliers final: 5 residues processed: 461 average time/residue: 0.3565 time to fit residues: 261.1356 Evaluate side-chains 316 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 310 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 195 ASN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 33 HIS ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.075173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059307 restraints weight = 107276.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060729 restraints weight = 62411.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061616 restraints weight = 43637.395| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24580 Z= 0.175 Angle : 0.945 20.480 33560 Z= 0.417 Chirality : 0.056 0.555 3964 Planarity : 0.005 0.059 4106 Dihedral : 16.181 108.432 5165 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.40 % Allowed : 5.61 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2836 helix: -0.70 (0.26), residues: 394 sheet: -0.99 (0.18), residues: 823 loop : -1.73 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 47 HIS 0.007 0.001 HIS C 374 PHE 0.019 0.002 PHE C 383 TYR 0.021 0.002 TYR C 217 ARG 0.014 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 54) link_NAG-ASN : angle 5.16771 ( 162) link_ALPHA1-4 : bond 0.01750 ( 4) link_ALPHA1-4 : angle 4.53737 ( 12) link_BETA1-2 : bond 0.00545 ( 1) link_BETA1-2 : angle 3.73406 ( 3) link_BETA1-4 : bond 0.01050 ( 31) link_BETA1-4 : angle 3.84974 ( 93) link_ALPHA1-3 : bond 0.01077 ( 4) link_ALPHA1-3 : angle 3.33319 ( 12) hydrogen bonds : bond 0.04228 ( 728) hydrogen bonds : angle 7.87107 ( 1980) link_BETA1-6 : bond 0.00312 ( 1) link_BETA1-6 : angle 3.24146 ( 3) SS BOND : bond 0.00486 ( 44) SS BOND : angle 2.26818 ( 88) link_BETA1-3 : bond 0.00395 ( 4) link_BETA1-3 : angle 4.85522 ( 12) covalent geometry : bond 0.00382 (24437) covalent geometry : angle 0.83375 (33175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 432 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8651 (tmm) cc_final: 0.8217 (tmm) REVERT: A 207 LYS cc_start: 0.7906 (pttp) cc_final: 0.7704 (pttt) REVERT: A 396 ILE cc_start: 0.7824 (pt) cc_final: 0.7474 (mm) REVERT: B 69 TRP cc_start: 0.5529 (t60) cc_final: 0.2979 (t60) REVERT: B 161 MET cc_start: 0.8447 (tpp) cc_final: 0.8028 (tpt) REVERT: B 175 LEU cc_start: 0.9027 (mt) cc_final: 0.8664 (mp) REVERT: B 277 ILE cc_start: 0.7465 (pt) cc_final: 0.7183 (pt) REVERT: B 492 GLU cc_start: 0.8333 (mp0) cc_final: 0.8050 (mm-30) REVERT: C 434 MET cc_start: 0.8557 (tmm) cc_final: 0.7850 (ttt) REVERT: D 601 LYS cc_start: 0.7337 (pttm) cc_final: 0.7121 (pttt) REVERT: D 637 ASN cc_start: 0.5910 (p0) cc_final: 0.5587 (t0) REVERT: E 596 TRP cc_start: 0.8540 (m-10) cc_final: 0.8204 (m-10) REVERT: F 640 GLN cc_start: 0.8758 (tp40) cc_final: 0.8174 (pm20) REVERT: H 80 MET cc_start: 0.8903 (tmm) cc_final: 0.8543 (tmm) REVERT: I 47 TRP cc_start: 0.8359 (t60) cc_final: 0.7398 (t60) REVERT: I 62 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8883 (ptmm) REVERT: I 80 MET cc_start: 0.8506 (tmm) cc_final: 0.6152 (tmm) REVERT: I 100 MET cc_start: 0.8716 (ptp) cc_final: 0.8142 (ptp) REVERT: K 75 ILE cc_start: 0.7992 (mm) cc_final: 0.7433 (tp) REVERT: L 51 VAL cc_start: 0.7397 (p) cc_final: 0.7156 (p) REVERT: L 86 TYR cc_start: 0.8367 (m-80) cc_final: 0.8019 (m-10) REVERT: M 36 TRP cc_start: 0.6641 (m100) cc_final: 0.6430 (m100) REVERT: M 37 ILE cc_start: 0.7989 (tp) cc_final: 0.7784 (tp) REVERT: M 51 ILE cc_start: 0.7394 (mt) cc_final: 0.6906 (tp) REVERT: M 72 ASP cc_start: 0.7196 (p0) cc_final: 0.6660 (p0) REVERT: N 46 GLU cc_start: 0.8078 (tt0) cc_final: 0.7753 (tt0) REVERT: O 5 GLN cc_start: 0.8918 (mm110) cc_final: 0.8664 (mt0) REVERT: O 51 ILE cc_start: 0.7329 (mm) cc_final: 0.6588 (tt) REVERT: O 78 LEU cc_start: 0.6303 (mm) cc_final: 0.5878 (tp) REVERT: O 91 TYR cc_start: 0.7054 (m-10) cc_final: 0.6675 (m-10) REVERT: O 100 TYR cc_start: 0.8171 (p90) cc_final: 0.6992 (p90) REVERT: Q 53 ASP cc_start: 0.8970 (t0) cc_final: 0.8746 (t0) REVERT: Q 85 ASP cc_start: 0.8135 (m-30) cc_final: 0.7935 (m-30) REVERT: Q 90 MET cc_start: 0.8463 (ttp) cc_final: 0.8230 (ttp) REVERT: R 66 PRO cc_start: 0.7836 (Cg_exo) cc_final: 0.7604 (Cg_endo) outliers start: 10 outliers final: 3 residues processed: 441 average time/residue: 0.3504 time to fit residues: 241.9458 Evaluate side-chains 300 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 41 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 85 HIS B 103 GLN B 249 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.072118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056310 restraints weight = 107304.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057659 restraints weight = 62055.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058507 restraints weight = 43715.363| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24580 Z= 0.228 Angle : 0.931 18.799 33560 Z= 0.416 Chirality : 0.055 0.445 3964 Planarity : 0.005 0.063 4106 Dihedral : 13.593 112.956 5165 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2836 helix: -1.00 (0.25), residues: 401 sheet: -0.94 (0.18), residues: 818 loop : -1.75 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 47 HIS 0.010 0.002 HIS C 72 PHE 0.026 0.002 PHE B 383 TYR 0.023 0.002 TYR C 217 ARG 0.010 0.001 ARG P 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 54) link_NAG-ASN : angle 4.88146 ( 162) link_ALPHA1-4 : bond 0.01553 ( 4) link_ALPHA1-4 : angle 4.94432 ( 12) link_BETA1-2 : bond 0.00430 ( 1) link_BETA1-2 : angle 4.04820 ( 3) link_BETA1-4 : bond 0.00835 ( 31) link_BETA1-4 : angle 3.63224 ( 93) link_ALPHA1-3 : bond 0.00772 ( 4) link_ALPHA1-3 : angle 3.34597 ( 12) hydrogen bonds : bond 0.04388 ( 728) hydrogen bonds : angle 7.36439 ( 1980) link_BETA1-6 : bond 0.00521 ( 1) link_BETA1-6 : angle 2.24268 ( 3) SS BOND : bond 0.00652 ( 44) SS BOND : angle 2.39700 ( 88) link_BETA1-3 : bond 0.00198 ( 4) link_BETA1-3 : angle 5.01797 ( 12) covalent geometry : bond 0.00508 (24437) covalent geometry : angle 0.82736 (33175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7833 (m-40) cc_final: 0.7581 (m-40) REVERT: A 382 PHE cc_start: 0.8268 (m-80) cc_final: 0.8067 (m-80) REVERT: A 396 ILE cc_start: 0.7907 (pt) cc_final: 0.7504 (mm) REVERT: A 443 ILE cc_start: 0.9142 (mm) cc_final: 0.8597 (tp) REVERT: B 69 TRP cc_start: 0.5002 (t60) cc_final: 0.3630 (t60) REVERT: B 161 MET cc_start: 0.8523 (tpp) cc_final: 0.7831 (tpt) REVERT: B 175 LEU cc_start: 0.9046 (mt) cc_final: 0.8660 (mp) REVERT: B 434 MET cc_start: 0.8974 (ttp) cc_final: 0.8713 (ttp) REVERT: B 443 ILE cc_start: 0.9094 (mm) cc_final: 0.8843 (mm) REVERT: B 492 GLU cc_start: 0.8384 (mp0) cc_final: 0.7898 (mm-30) REVERT: C 434 MET cc_start: 0.8541 (tmm) cc_final: 0.8074 (ttt) REVERT: D 575 GLN cc_start: 0.8073 (tt0) cc_final: 0.7826 (tm-30) REVERT: D 637 ASN cc_start: 0.5886 (p0) cc_final: 0.5546 (t0) REVERT: E 648 GLU cc_start: 0.7954 (tp30) cc_final: 0.7723 (mm-30) REVERT: F 595 ILE cc_start: 0.8705 (tp) cc_final: 0.8481 (tp) REVERT: F 619 LEU cc_start: 0.8029 (tt) cc_final: 0.7673 (tp) REVERT: H 77 ILE cc_start: 0.8779 (mm) cc_final: 0.8535 (mm) REVERT: I 45 LEU cc_start: 0.7999 (tp) cc_final: 0.7761 (tp) REVERT: I 47 TRP cc_start: 0.8556 (t60) cc_final: 0.7775 (t60) REVERT: I 80 MET cc_start: 0.8424 (tmm) cc_final: 0.6092 (tmm) REVERT: I 100 MET cc_start: 0.8829 (ptp) cc_final: 0.8222 (ptp) REVERT: L 51 VAL cc_start: 0.7508 (p) cc_final: 0.7255 (p) REVERT: M 33 TYR cc_start: 0.6556 (m-80) cc_final: 0.6031 (m-80) REVERT: M 51 ILE cc_start: 0.7696 (mt) cc_final: 0.7202 (tp) REVERT: M 72 ASP cc_start: 0.7465 (p0) cc_final: 0.7137 (p0) REVERT: M 100 TYR cc_start: 0.6173 (p90) cc_final: 0.5881 (p90) REVERT: N 100 MET cc_start: 0.8869 (mpp) cc_final: 0.8244 (mpp) REVERT: O 78 LEU cc_start: 0.6329 (mm) cc_final: 0.5886 (tp) REVERT: O 91 TYR cc_start: 0.7504 (m-10) cc_final: 0.6722 (m-10) REVERT: O 105 LYS cc_start: 0.7736 (tppt) cc_final: 0.7287 (mtmm) REVERT: P 46 LEU cc_start: 0.7981 (pt) cc_final: 0.7508 (tt) REVERT: Q 53 ASP cc_start: 0.8976 (t0) cc_final: 0.8760 (t0) REVERT: Q 90 MET cc_start: 0.8127 (ttp) cc_final: 0.7905 (ttp) REVERT: R 48 ILE cc_start: 0.8228 (mt) cc_final: 0.8021 (mt) outliers start: 2 outliers final: 1 residues processed: 399 average time/residue: 0.3456 time to fit residues: 217.3841 Evaluate side-chains 292 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 196 optimal weight: 0.0060 chunk 105 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN B 195 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055177 restraints weight = 108877.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056515 restraints weight = 63155.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.057368 restraints weight = 44592.830| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 24580 Z= 0.219 Angle : 0.881 17.365 33560 Z= 0.398 Chirality : 0.053 0.452 3964 Planarity : 0.005 0.064 4106 Dihedral : 12.395 104.730 5165 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2836 helix: -1.05 (0.25), residues: 401 sheet: -1.01 (0.18), residues: 820 loop : -1.72 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 47 HIS 0.007 0.001 HIS C 374 PHE 0.027 0.002 PHE B 383 TYR 0.029 0.002 TYR C 217 ARG 0.007 0.001 ARG Q 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 54) link_NAG-ASN : angle 4.46660 ( 162) link_ALPHA1-4 : bond 0.02034 ( 4) link_ALPHA1-4 : angle 4.30314 ( 12) link_BETA1-2 : bond 0.00161 ( 1) link_BETA1-2 : angle 3.90183 ( 3) link_BETA1-4 : bond 0.00819 ( 31) link_BETA1-4 : angle 3.49461 ( 93) link_ALPHA1-3 : bond 0.00806 ( 4) link_ALPHA1-3 : angle 3.35093 ( 12) hydrogen bonds : bond 0.03927 ( 728) hydrogen bonds : angle 6.99391 ( 1980) link_BETA1-6 : bond 0.00326 ( 1) link_BETA1-6 : angle 2.29612 ( 3) SS BOND : bond 0.00513 ( 44) SS BOND : angle 2.34650 ( 88) link_BETA1-3 : bond 0.00341 ( 4) link_BETA1-3 : angle 4.85603 ( 12) covalent geometry : bond 0.00494 (24437) covalent geometry : angle 0.78564 (33175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7681 (m110) cc_final: 0.7426 (m-40) REVERT: A 396 ILE cc_start: 0.7964 (pt) cc_final: 0.7587 (mm) REVERT: A 443 ILE cc_start: 0.9175 (mm) cc_final: 0.8717 (tp) REVERT: B 69 TRP cc_start: 0.5171 (t60) cc_final: 0.2960 (t60) REVERT: B 104 MET cc_start: 0.8444 (tpp) cc_final: 0.7927 (tpp) REVERT: B 161 MET cc_start: 0.8486 (tpp) cc_final: 0.7915 (tpt) REVERT: B 175 LEU cc_start: 0.8998 (mt) cc_final: 0.8707 (mp) REVERT: B 434 MET cc_start: 0.8963 (ttp) cc_final: 0.8672 (ttp) REVERT: B 492 GLU cc_start: 0.8447 (mp0) cc_final: 0.7931 (mm-30) REVERT: C 434 MET cc_start: 0.8511 (tmm) cc_final: 0.8192 (ttt) REVERT: D 637 ASN cc_start: 0.5763 (p0) cc_final: 0.5528 (t0) REVERT: D 655 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7287 (mtpt) REVERT: F 619 LEU cc_start: 0.8085 (tt) cc_final: 0.7836 (tp) REVERT: H 77 ILE cc_start: 0.8806 (mm) cc_final: 0.8599 (mm) REVERT: H 80 MET cc_start: 0.8797 (tmm) cc_final: 0.8406 (tmm) REVERT: H 97 PHE cc_start: 0.7976 (m-80) cc_final: 0.7591 (m-80) REVERT: H 100 MET cc_start: 0.8578 (ptt) cc_final: 0.8266 (ptt) REVERT: I 47 TRP cc_start: 0.8478 (t60) cc_final: 0.7828 (t60) REVERT: I 48 MET cc_start: 0.8563 (mmm) cc_final: 0.8277 (mmm) REVERT: I 80 MET cc_start: 0.8407 (tmm) cc_final: 0.6143 (tmm) REVERT: I 100 MET cc_start: 0.8916 (ptp) cc_final: 0.8318 (ptp) REVERT: M 51 ILE cc_start: 0.7788 (mt) cc_final: 0.7159 (tp) REVERT: M 72 ASP cc_start: 0.7730 (p0) cc_final: 0.7079 (p0) REVERT: N 46 GLU cc_start: 0.8118 (tt0) cc_final: 0.7664 (tt0) REVERT: N 51 ILE cc_start: 0.7150 (tp) cc_final: 0.6838 (tp) REVERT: N 100 MET cc_start: 0.8937 (mpp) cc_final: 0.8129 (mpp) REVERT: O 37 ILE cc_start: 0.8554 (mm) cc_final: 0.8331 (mm) REVERT: O 47 TRP cc_start: 0.5430 (p90) cc_final: 0.5229 (p90) REVERT: O 78 LEU cc_start: 0.6398 (mm) cc_final: 0.5870 (tp) REVERT: O 105 LYS cc_start: 0.7842 (tppt) cc_final: 0.7473 (mtmm) REVERT: P 46 LEU cc_start: 0.7925 (pt) cc_final: 0.7507 (tt) REVERT: Q 90 MET cc_start: 0.8163 (ttp) cc_final: 0.7907 (ttp) REVERT: R 90 MET cc_start: 0.7320 (tmm) cc_final: 0.6703 (tmm) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.3436 time to fit residues: 204.5907 Evaluate side-chains 277 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 114 optimal weight: 0.0050 chunk 109 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.070947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055919 restraints weight = 108242.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057074 restraints weight = 62772.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.058102 restraints weight = 41587.428| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24580 Z= 0.172 Angle : 0.840 16.934 33560 Z= 0.380 Chirality : 0.052 0.439 3964 Planarity : 0.004 0.050 4106 Dihedral : 11.773 106.209 5165 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.15), residues: 2836 helix: -0.88 (0.25), residues: 392 sheet: -0.88 (0.19), residues: 786 loop : -1.70 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 47 HIS 0.010 0.001 HIS A 66 PHE 0.021 0.002 PHE B 383 TYR 0.019 0.002 TYR C 217 ARG 0.007 0.001 ARG O 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 54) link_NAG-ASN : angle 4.12111 ( 162) link_ALPHA1-4 : bond 0.01882 ( 4) link_ALPHA1-4 : angle 4.03986 ( 12) link_BETA1-2 : bond 0.00215 ( 1) link_BETA1-2 : angle 3.22469 ( 3) link_BETA1-4 : bond 0.00785 ( 31) link_BETA1-4 : angle 3.43228 ( 93) link_ALPHA1-3 : bond 0.00803 ( 4) link_ALPHA1-3 : angle 3.30900 ( 12) hydrogen bonds : bond 0.03677 ( 728) hydrogen bonds : angle 6.73016 ( 1980) link_BETA1-6 : bond 0.00407 ( 1) link_BETA1-6 : angle 2.40936 ( 3) SS BOND : bond 0.00547 ( 44) SS BOND : angle 2.37411 ( 88) link_BETA1-3 : bond 0.00211 ( 4) link_BETA1-3 : angle 4.71391 ( 12) covalent geometry : bond 0.00387 (24437) covalent geometry : angle 0.75095 (33175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7723 (m110) cc_final: 0.7497 (m-40) REVERT: A 396 ILE cc_start: 0.7978 (pt) cc_final: 0.7611 (mm) REVERT: A 443 ILE cc_start: 0.9127 (mm) cc_final: 0.8740 (tp) REVERT: B 69 TRP cc_start: 0.5277 (t60) cc_final: 0.3001 (t60) REVERT: B 104 MET cc_start: 0.8406 (tpp) cc_final: 0.7887 (tpp) REVERT: B 161 MET cc_start: 0.8488 (tpp) cc_final: 0.7938 (tpt) REVERT: B 175 LEU cc_start: 0.9094 (mt) cc_final: 0.8806 (mp) REVERT: B 434 MET cc_start: 0.8959 (ttp) cc_final: 0.8653 (ttp) REVERT: B 492 GLU cc_start: 0.8457 (mp0) cc_final: 0.7965 (mm-30) REVERT: C 271 MET cc_start: 0.7175 (mtp) cc_final: 0.6732 (ttt) REVERT: C 434 MET cc_start: 0.8163 (tmm) cc_final: 0.7814 (ttt) REVERT: C 494 LEU cc_start: 0.9064 (pp) cc_final: 0.8493 (pp) REVERT: D 575 GLN cc_start: 0.8042 (tt0) cc_final: 0.7805 (tm-30) REVERT: D 637 ASN cc_start: 0.5900 (p0) cc_final: 0.5615 (t0) REVERT: F 595 ILE cc_start: 0.8632 (tp) cc_final: 0.8388 (tp) REVERT: H 77 ILE cc_start: 0.8867 (mm) cc_final: 0.8595 (mm) REVERT: I 47 TRP cc_start: 0.8538 (t60) cc_final: 0.7850 (t60) REVERT: I 80 MET cc_start: 0.8374 (tmm) cc_final: 0.6134 (tmm) REVERT: I 100 MET cc_start: 0.8890 (ptp) cc_final: 0.8218 (ptp) REVERT: K 75 ILE cc_start: 0.8382 (mm) cc_final: 0.7662 (mm) REVERT: M 5 GLN cc_start: 0.7245 (pm20) cc_final: 0.6897 (pp30) REVERT: M 33 TYR cc_start: 0.6965 (m-80) cc_final: 0.6626 (m-80) REVERT: M 51 ILE cc_start: 0.7417 (mt) cc_final: 0.7091 (tp) REVERT: M 91 TYR cc_start: 0.4907 (m-10) cc_final: 0.4657 (m-10) REVERT: N 46 GLU cc_start: 0.8145 (tt0) cc_final: 0.7643 (tt0) REVERT: N 51 ILE cc_start: 0.7123 (tp) cc_final: 0.6823 (tp) REVERT: N 100 MET cc_start: 0.8967 (mpp) cc_final: 0.8239 (mpp) REVERT: O 46 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7674 (tt0) REVERT: O 78 LEU cc_start: 0.6210 (mm) cc_final: 0.5720 (tp) REVERT: O 91 TYR cc_start: 0.7498 (m-10) cc_final: 0.7068 (m-10) REVERT: P 46 LEU cc_start: 0.7976 (pt) cc_final: 0.7535 (tt) REVERT: Q 90 MET cc_start: 0.8104 (ttp) cc_final: 0.7876 (ttp) REVERT: R 38 HIS cc_start: 0.7682 (t-90) cc_final: 0.7391 (t70) REVERT: R 47 LEU cc_start: 0.8571 (mp) cc_final: 0.8262 (mp) REVERT: R 90 MET cc_start: 0.7366 (tmm) cc_final: 0.6941 (tmm) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.3361 time to fit residues: 204.7132 Evaluate side-chains 290 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 103 GLN B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055325 restraints weight = 107929.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056652 restraints weight = 62798.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057473 restraints weight = 44447.226| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24580 Z= 0.161 Angle : 0.832 17.522 33560 Z= 0.376 Chirality : 0.052 0.426 3964 Planarity : 0.004 0.045 4106 Dihedral : 11.176 103.882 5165 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2836 helix: -0.83 (0.26), residues: 395 sheet: -0.96 (0.18), residues: 807 loop : -1.60 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 47 HIS 0.006 0.001 HIS L 39 PHE 0.021 0.002 PHE C 383 TYR 0.021 0.001 TYR A 217 ARG 0.010 0.001 ARG M 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 54) link_NAG-ASN : angle 4.16128 ( 162) link_ALPHA1-4 : bond 0.02086 ( 4) link_ALPHA1-4 : angle 3.94453 ( 12) link_BETA1-2 : bond 0.00126 ( 1) link_BETA1-2 : angle 3.10313 ( 3) link_BETA1-4 : bond 0.00785 ( 31) link_BETA1-4 : angle 3.38143 ( 93) link_ALPHA1-3 : bond 0.00849 ( 4) link_ALPHA1-3 : angle 3.31073 ( 12) hydrogen bonds : bond 0.03602 ( 728) hydrogen bonds : angle 6.59504 ( 1980) link_BETA1-6 : bond 0.00243 ( 1) link_BETA1-6 : angle 2.44286 ( 3) SS BOND : bond 0.00579 ( 44) SS BOND : angle 2.41968 ( 88) link_BETA1-3 : bond 0.00276 ( 4) link_BETA1-3 : angle 4.50858 ( 12) covalent geometry : bond 0.00362 (24437) covalent geometry : angle 0.74104 (33175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7639 (m110) cc_final: 0.7388 (m-40) REVERT: A 396 ILE cc_start: 0.7785 (pt) cc_final: 0.7387 (mm) REVERT: A 443 ILE cc_start: 0.9037 (mm) cc_final: 0.8785 (tp) REVERT: B 69 TRP cc_start: 0.5374 (t60) cc_final: 0.3005 (t60) REVERT: B 161 MET cc_start: 0.8472 (tpp) cc_final: 0.7942 (tpt) REVERT: B 175 LEU cc_start: 0.9063 (mt) cc_final: 0.8830 (mp) REVERT: B 434 MET cc_start: 0.8941 (ttp) cc_final: 0.8666 (ttp) REVERT: B 492 GLU cc_start: 0.8466 (mp0) cc_final: 0.7955 (mm-30) REVERT: C 180 ASP cc_start: 0.8453 (m-30) cc_final: 0.8193 (m-30) REVERT: C 434 MET cc_start: 0.8330 (tmm) cc_final: 0.7872 (ttt) REVERT: D 575 GLN cc_start: 0.8067 (tt0) cc_final: 0.7783 (tm-30) REVERT: D 637 ASN cc_start: 0.5664 (p0) cc_final: 0.5235 (t0) REVERT: I 47 TRP cc_start: 0.8553 (t60) cc_final: 0.7957 (t60) REVERT: I 48 MET cc_start: 0.8648 (mmm) cc_final: 0.8374 (mmm) REVERT: I 80 MET cc_start: 0.8333 (tmm) cc_final: 0.6118 (tmm) REVERT: I 100 MET cc_start: 0.8898 (ptp) cc_final: 0.8224 (ptp) REVERT: M 3 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7459 (tm-30) REVERT: M 5 GLN cc_start: 0.7022 (pm20) cc_final: 0.6747 (pm20) REVERT: M 29 MET cc_start: 0.1272 (mtm) cc_final: 0.0964 (mtm) REVERT: M 33 TYR cc_start: 0.7021 (m-80) cc_final: 0.6484 (m-80) REVERT: M 51 ILE cc_start: 0.7490 (mt) cc_final: 0.7026 (tp) REVERT: N 46 GLU cc_start: 0.8131 (tt0) cc_final: 0.7649 (tt0) REVERT: N 51 ILE cc_start: 0.7141 (tp) cc_final: 0.6834 (tp) REVERT: N 100 MET cc_start: 0.8936 (mpp) cc_final: 0.8254 (mpp) REVERT: O 13 LYS cc_start: 0.8917 (pttm) cc_final: 0.8651 (mtmm) REVERT: O 22 CYS cc_start: 0.5885 (t) cc_final: 0.5661 (t) REVERT: O 78 LEU cc_start: 0.6258 (mm) cc_final: 0.5791 (tp) REVERT: O 91 TYR cc_start: 0.7615 (m-10) cc_final: 0.6968 (m-10) REVERT: P 46 LEU cc_start: 0.7901 (pt) cc_final: 0.7489 (tt) REVERT: Q 90 MET cc_start: 0.8090 (ttp) cc_final: 0.7863 (ttp) REVERT: R 47 LEU cc_start: 0.8681 (mp) cc_final: 0.8385 (mp) REVERT: R 90 MET cc_start: 0.7214 (tmm) cc_final: 0.6896 (tmm) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.3186 time to fit residues: 198.5621 Evaluate side-chains 281 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 182 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 270 optimal weight: 0.0570 chunk 71 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 219 optimal weight: 0.0370 chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055439 restraints weight = 107869.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056751 restraints weight = 62485.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057574 restraints weight = 44037.955| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24580 Z= 0.152 Angle : 0.817 17.553 33560 Z= 0.370 Chirality : 0.051 0.413 3964 Planarity : 0.004 0.045 4106 Dihedral : 10.673 103.006 5165 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2836 helix: -0.77 (0.26), residues: 395 sheet: -0.86 (0.18), residues: 803 loop : -1.62 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 47 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE C 233 TYR 0.032 0.002 TYR A 217 ARG 0.011 0.000 ARG M 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 54) link_NAG-ASN : angle 3.82950 ( 162) link_ALPHA1-4 : bond 0.02242 ( 4) link_ALPHA1-4 : angle 4.10026 ( 12) link_BETA1-2 : bond 0.00091 ( 1) link_BETA1-2 : angle 3.00122 ( 3) link_BETA1-4 : bond 0.00773 ( 31) link_BETA1-4 : angle 3.35847 ( 93) link_ALPHA1-3 : bond 0.00872 ( 4) link_ALPHA1-3 : angle 3.33143 ( 12) hydrogen bonds : bond 0.03522 ( 728) hydrogen bonds : angle 6.46471 ( 1980) link_BETA1-6 : bond 0.00161 ( 1) link_BETA1-6 : angle 2.45411 ( 3) SS BOND : bond 0.00524 ( 44) SS BOND : angle 2.50812 ( 88) link_BETA1-3 : bond 0.00302 ( 4) link_BETA1-3 : angle 4.23878 ( 12) covalent geometry : bond 0.00343 (24437) covalent geometry : angle 0.73337 (33175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7650 (m110) cc_final: 0.7415 (m-40) REVERT: A 396 ILE cc_start: 0.7782 (pt) cc_final: 0.7389 (mm) REVERT: A 443 ILE cc_start: 0.9003 (mm) cc_final: 0.8774 (tp) REVERT: B 69 TRP cc_start: 0.5390 (t60) cc_final: 0.3023 (t60) REVERT: B 161 MET cc_start: 0.8430 (tpp) cc_final: 0.7932 (tpt) REVERT: B 175 LEU cc_start: 0.9074 (mt) cc_final: 0.8860 (mp) REVERT: B 434 MET cc_start: 0.8972 (ttp) cc_final: 0.8718 (ttp) REVERT: B 492 GLU cc_start: 0.8456 (mp0) cc_final: 0.8054 (mm-30) REVERT: C 180 ASP cc_start: 0.8455 (m-30) cc_final: 0.8214 (m-30) REVERT: C 434 MET cc_start: 0.8293 (tmm) cc_final: 0.7788 (ttt) REVERT: D 575 GLN cc_start: 0.8123 (tt0) cc_final: 0.7748 (tm-30) REVERT: D 637 ASN cc_start: 0.5830 (p0) cc_final: 0.5476 (t0) REVERT: D 638 TYR cc_start: 0.7523 (m-80) cc_final: 0.7131 (m-80) REVERT: D 651 ASN cc_start: 0.5280 (m110) cc_final: 0.4998 (m110) REVERT: E 530 MET cc_start: 0.7369 (mtm) cc_final: 0.7063 (mtm) REVERT: E 648 GLU cc_start: 0.7952 (tp30) cc_final: 0.7693 (mm-30) REVERT: F 534 SER cc_start: 0.8992 (m) cc_final: 0.8755 (m) REVERT: H 77 ILE cc_start: 0.8805 (mm) cc_final: 0.8556 (mm) REVERT: H 80 MET cc_start: 0.8610 (tmm) cc_final: 0.8191 (tmm) REVERT: I 47 TRP cc_start: 0.8526 (t60) cc_final: 0.7948 (t60) REVERT: I 48 MET cc_start: 0.8695 (mmm) cc_final: 0.8395 (mmm) REVERT: I 80 MET cc_start: 0.8348 (tmm) cc_final: 0.6255 (tmm) REVERT: I 100 MET cc_start: 0.8899 (ptp) cc_final: 0.8249 (ptp) REVERT: M 5 GLN cc_start: 0.6976 (pm20) cc_final: 0.6625 (pp30) REVERT: M 33 TYR cc_start: 0.7059 (m-80) cc_final: 0.6427 (m-80) REVERT: M 51 ILE cc_start: 0.7587 (mt) cc_final: 0.7128 (tp) REVERT: N 46 GLU cc_start: 0.8095 (tt0) cc_final: 0.7637 (tt0) REVERT: N 51 ILE cc_start: 0.7145 (tp) cc_final: 0.6851 (tp) REVERT: N 100 MET cc_start: 0.8984 (mpp) cc_final: 0.8263 (mpp) REVERT: O 13 LYS cc_start: 0.8915 (pttm) cc_final: 0.8666 (mtmm) REVERT: O 22 CYS cc_start: 0.5702 (t) cc_final: 0.5466 (t) REVERT: O 78 LEU cc_start: 0.6218 (mm) cc_final: 0.5726 (tp) REVERT: O 91 TYR cc_start: 0.7593 (m-10) cc_final: 0.6995 (m-10) REVERT: P 46 LEU cc_start: 0.7861 (pt) cc_final: 0.7496 (tt) REVERT: Q 90 MET cc_start: 0.8111 (ttp) cc_final: 0.7895 (ttp) REVERT: R 47 LEU cc_start: 0.8678 (mp) cc_final: 0.8353 (mp) REVERT: R 90 MET cc_start: 0.7232 (tmm) cc_final: 0.6944 (tmm) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.3316 time to fit residues: 205.5632 Evaluate side-chains 286 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 170 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 280 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 85 HIS B 478 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054152 restraints weight = 109062.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055442 restraints weight = 63116.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056256 restraints weight = 44428.332| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24580 Z= 0.201 Angle : 0.867 17.518 33560 Z= 0.395 Chirality : 0.052 0.417 3964 Planarity : 0.005 0.091 4106 Dihedral : 10.450 100.563 5165 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 2836 helix: -0.82 (0.26), residues: 392 sheet: -0.89 (0.18), residues: 799 loop : -1.70 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP O 47 HIS 0.006 0.001 HIS R 38 PHE 0.024 0.002 PHE C 383 TYR 0.024 0.002 TYR F 586 ARG 0.011 0.001 ARG M 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 54) link_NAG-ASN : angle 4.05321 ( 162) link_ALPHA1-4 : bond 0.02147 ( 4) link_ALPHA1-4 : angle 4.34643 ( 12) link_BETA1-2 : bond 0.00122 ( 1) link_BETA1-2 : angle 3.10930 ( 3) link_BETA1-4 : bond 0.00810 ( 31) link_BETA1-4 : angle 3.49100 ( 93) link_ALPHA1-3 : bond 0.00844 ( 4) link_ALPHA1-3 : angle 3.41308 ( 12) hydrogen bonds : bond 0.03718 ( 728) hydrogen bonds : angle 6.46964 ( 1980) link_BETA1-6 : bond 0.00081 ( 1) link_BETA1-6 : angle 2.39015 ( 3) SS BOND : bond 0.00588 ( 44) SS BOND : angle 2.63319 ( 88) link_BETA1-3 : bond 0.00389 ( 4) link_BETA1-3 : angle 3.99347 ( 12) covalent geometry : bond 0.00458 (24437) covalent geometry : angle 0.78119 (33175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7642 (m110) cc_final: 0.7376 (m-40) REVERT: A 396 ILE cc_start: 0.7892 (pt) cc_final: 0.7598 (mm) REVERT: B 69 TRP cc_start: 0.5463 (t60) cc_final: 0.2978 (t60) REVERT: B 161 MET cc_start: 0.8442 (tpp) cc_final: 0.7899 (tpt) REVERT: B 175 LEU cc_start: 0.9086 (mt) cc_final: 0.8830 (mp) REVERT: B 359 ILE cc_start: 0.8742 (mt) cc_final: 0.8509 (mm) REVERT: B 434 MET cc_start: 0.8937 (ttp) cc_final: 0.8600 (ttp) REVERT: B 492 GLU cc_start: 0.8421 (mp0) cc_final: 0.7948 (mm-30) REVERT: C 434 MET cc_start: 0.8374 (tmm) cc_final: 0.7931 (ttt) REVERT: C 494 LEU cc_start: 0.9076 (pp) cc_final: 0.8696 (pp) REVERT: D 637 ASN cc_start: 0.5759 (p0) cc_final: 0.5324 (t0) REVERT: E 648 GLU cc_start: 0.7834 (tp30) cc_final: 0.7526 (mm-30) REVERT: F 595 ILE cc_start: 0.8689 (tp) cc_final: 0.8199 (tp) REVERT: F 596 TRP cc_start: 0.8347 (m-10) cc_final: 0.7459 (m-10) REVERT: F 643 TYR cc_start: 0.7958 (m-10) cc_final: 0.7545 (m-10) REVERT: H 77 ILE cc_start: 0.8860 (mm) cc_final: 0.8647 (mm) REVERT: H 80 MET cc_start: 0.8656 (tmm) cc_final: 0.8220 (tmm) REVERT: I 47 TRP cc_start: 0.8399 (t60) cc_final: 0.7655 (t60) REVERT: I 48 MET cc_start: 0.8554 (mmm) cc_final: 0.8236 (mmm) REVERT: I 80 MET cc_start: 0.8381 (tmm) cc_final: 0.6285 (tmm) REVERT: K 61 ARG cc_start: 0.6614 (ptm-80) cc_final: 0.6407 (ptm-80) REVERT: M 3 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7366 (tm-30) REVERT: M 33 TYR cc_start: 0.7029 (m-80) cc_final: 0.6472 (m-80) REVERT: M 50 TYR cc_start: 0.6727 (p90) cc_final: 0.6436 (p90) REVERT: M 51 ILE cc_start: 0.7791 (mt) cc_final: 0.7325 (tp) REVERT: N 46 GLU cc_start: 0.8155 (tt0) cc_final: 0.7702 (tt0) REVERT: N 77 GLN cc_start: 0.7524 (pm20) cc_final: 0.7165 (pm20) REVERT: N 100 MET cc_start: 0.8966 (mpp) cc_final: 0.8272 (mpp) REVERT: O 13 LYS cc_start: 0.8919 (pttm) cc_final: 0.8646 (mtmm) REVERT: O 22 CYS cc_start: 0.5566 (t) cc_final: 0.5353 (t) REVERT: O 37 ILE cc_start: 0.8674 (mm) cc_final: 0.8447 (mm) REVERT: O 47 TRP cc_start: 0.5076 (p90) cc_final: 0.4832 (p90) REVERT: O 78 LEU cc_start: 0.6189 (mm) cc_final: 0.5743 (tp) REVERT: O 91 TYR cc_start: 0.7661 (m-10) cc_final: 0.7082 (m-10) REVERT: P 46 LEU cc_start: 0.7987 (pt) cc_final: 0.7622 (tt) REVERT: Q 90 MET cc_start: 0.8057 (ttp) cc_final: 0.7856 (ttp) REVERT: R 38 HIS cc_start: 0.7770 (t-90) cc_final: 0.7503 (t70) REVERT: R 47 LEU cc_start: 0.8726 (mp) cc_final: 0.8441 (mp) REVERT: R 90 MET cc_start: 0.7276 (tmm) cc_final: 0.6998 (tmm) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.3235 time to fit residues: 188.8586 Evaluate side-chains 288 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 228 optimal weight: 10.0000 chunk 125 optimal weight: 0.0270 chunk 235 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 66 HIS B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66CASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056286 restraints weight = 108266.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057616 restraints weight = 62988.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058423 restraints weight = 41803.650| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24580 Z= 0.131 Angle : 0.813 17.029 33560 Z= 0.369 Chirality : 0.051 0.403 3964 Planarity : 0.004 0.074 4106 Dihedral : 9.861 100.975 5165 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.15), residues: 2836 helix: -0.62 (0.26), residues: 386 sheet: -0.85 (0.18), residues: 795 loop : -1.60 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 47 HIS 0.004 0.001 HIS P 89 PHE 0.018 0.001 PHE C 383 TYR 0.020 0.002 TYR F 586 ARG 0.014 0.001 ARG O 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 54) link_NAG-ASN : angle 3.67802 ( 162) link_ALPHA1-4 : bond 0.01990 ( 4) link_ALPHA1-4 : angle 4.23927 ( 12) link_BETA1-2 : bond 0.00035 ( 1) link_BETA1-2 : angle 3.10187 ( 3) link_BETA1-4 : bond 0.00771 ( 31) link_BETA1-4 : angle 3.47949 ( 93) link_ALPHA1-3 : bond 0.00778 ( 4) link_ALPHA1-3 : angle 3.30272 ( 12) hydrogen bonds : bond 0.03391 ( 728) hydrogen bonds : angle 6.35849 ( 1980) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 2.54834 ( 3) SS BOND : bond 0.00534 ( 44) SS BOND : angle 2.53538 ( 88) link_BETA1-3 : bond 0.00359 ( 4) link_BETA1-3 : angle 4.17497 ( 12) covalent geometry : bond 0.00295 (24437) covalent geometry : angle 0.72994 (33175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7512 (m-40) cc_final: 0.7215 (m-40) REVERT: A 396 ILE cc_start: 0.7887 (pt) cc_final: 0.7647 (mm) REVERT: B 69 TRP cc_start: 0.5327 (t60) cc_final: 0.2869 (t60) REVERT: B 161 MET cc_start: 0.8382 (tpp) cc_final: 0.8040 (tpt) REVERT: B 175 LEU cc_start: 0.9137 (mt) cc_final: 0.8867 (mp) REVERT: B 265 LEU cc_start: 0.6182 (tp) cc_final: 0.5791 (tp) REVERT: B 287 GLN cc_start: 0.8392 (tt0) cc_final: 0.7864 (tt0) REVERT: B 359 ILE cc_start: 0.8676 (mt) cc_final: 0.8411 (mm) REVERT: B 434 MET cc_start: 0.8933 (ttp) cc_final: 0.8701 (ttp) REVERT: B 492 GLU cc_start: 0.8410 (mp0) cc_final: 0.8022 (mm-30) REVERT: C 434 MET cc_start: 0.8100 (tmm) cc_final: 0.7616 (ttt) REVERT: C 494 LEU cc_start: 0.9121 (pp) cc_final: 0.8681 (pp) REVERT: D 637 ASN cc_start: 0.5686 (p0) cc_final: 0.5229 (t0) REVERT: D 638 TYR cc_start: 0.7705 (m-80) cc_final: 0.7279 (m-80) REVERT: E 530 MET cc_start: 0.7354 (mtm) cc_final: 0.6971 (mtm) REVERT: F 534 SER cc_start: 0.8978 (m) cc_final: 0.8737 (m) REVERT: F 538 THR cc_start: 0.7976 (m) cc_final: 0.7761 (t) REVERT: F 595 ILE cc_start: 0.8532 (tp) cc_final: 0.8198 (tp) REVERT: F 596 TRP cc_start: 0.8218 (m-10) cc_final: 0.7170 (m-10) REVERT: F 643 TYR cc_start: 0.7960 (m-10) cc_final: 0.7593 (m-10) REVERT: H 48 MET cc_start: 0.7641 (mmm) cc_final: 0.7302 (mmm) REVERT: H 77 ILE cc_start: 0.8795 (mm) cc_final: 0.8585 (mm) REVERT: I 46 GLU cc_start: 0.6424 (mp0) cc_final: 0.6125 (mp0) REVERT: I 47 TRP cc_start: 0.8312 (t60) cc_final: 0.7648 (t60) REVERT: I 48 MET cc_start: 0.8539 (mmm) cc_final: 0.8242 (mmm) REVERT: I 80 MET cc_start: 0.8394 (tmm) cc_final: 0.6251 (tmm) REVERT: I 87 THR cc_start: 0.8809 (m) cc_final: 0.8507 (p) REVERT: K 61 ARG cc_start: 0.6551 (ptm-80) cc_final: 0.6315 (ptm-80) REVERT: L 45 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8902 (mtmt) REVERT: L 46 LEU cc_start: 0.7957 (tp) cc_final: 0.7699 (tp) REVERT: M 3 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7241 (tm-30) REVERT: M 33 TYR cc_start: 0.7044 (m-80) cc_final: 0.6180 (m-80) REVERT: M 50 TYR cc_start: 0.6581 (p90) cc_final: 0.6281 (p90) REVERT: M 51 ILE cc_start: 0.7745 (mt) cc_final: 0.7285 (tp) REVERT: N 46 GLU cc_start: 0.8162 (tt0) cc_final: 0.7821 (tt0) REVERT: N 77 GLN cc_start: 0.7299 (pm20) cc_final: 0.7056 (pm20) REVERT: N 100 MET cc_start: 0.8930 (mpp) cc_final: 0.8209 (mpp) REVERT: O 13 LYS cc_start: 0.8926 (pttm) cc_final: 0.8723 (mtmm) REVERT: O 50 TYR cc_start: 0.5134 (t80) cc_final: 0.4841 (t80) REVERT: O 91 TYR cc_start: 0.7652 (m-10) cc_final: 0.7113 (m-10) REVERT: O 100 TYR cc_start: 0.8005 (m-10) cc_final: 0.7673 (m-80) REVERT: P 46 LEU cc_start: 0.7929 (pt) cc_final: 0.7649 (tt) REVERT: Q 90 MET cc_start: 0.8090 (ttp) cc_final: 0.7846 (ttp) REVERT: R 47 LEU cc_start: 0.8688 (mp) cc_final: 0.8378 (mp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3377 time to fit residues: 209.0968 Evaluate side-chains 296 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 38 optimal weight: 10.0000 chunk 204 optimal weight: 0.0770 chunk 26 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 195 optimal weight: 0.1980 chunk 223 optimal weight: 0.0030 chunk 8 optimal weight: 0.4980 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 66CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.072153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056663 restraints weight = 108168.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058053 restraints weight = 61771.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058894 restraints weight = 42959.707| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24580 Z= 0.125 Angle : 0.789 16.843 33560 Z= 0.360 Chirality : 0.050 0.425 3964 Planarity : 0.004 0.062 4106 Dihedral : 9.411 101.092 5165 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.08 % Allowed : 0.36 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2836 helix: -0.51 (0.27), residues: 383 sheet: -0.67 (0.19), residues: 777 loop : -1.57 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 47 HIS 0.004 0.001 HIS P 89 PHE 0.016 0.001 PHE C 383 TYR 0.019 0.001 TYR F 586 ARG 0.007 0.000 ARG M 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 54) link_NAG-ASN : angle 3.48896 ( 162) link_ALPHA1-4 : bond 0.02034 ( 4) link_ALPHA1-4 : angle 4.22541 ( 12) link_BETA1-2 : bond 0.00066 ( 1) link_BETA1-2 : angle 3.00208 ( 3) link_BETA1-4 : bond 0.00761 ( 31) link_BETA1-4 : angle 3.28118 ( 93) link_ALPHA1-3 : bond 0.00787 ( 4) link_ALPHA1-3 : angle 3.25609 ( 12) hydrogen bonds : bond 0.03332 ( 728) hydrogen bonds : angle 6.21202 ( 1980) link_BETA1-6 : bond 0.00181 ( 1) link_BETA1-6 : angle 2.54621 ( 3) SS BOND : bond 0.00516 ( 44) SS BOND : angle 2.46117 ( 88) link_BETA1-3 : bond 0.00443 ( 4) link_BETA1-3 : angle 4.08556 ( 12) covalent geometry : bond 0.00275 (24437) covalent geometry : angle 0.71199 (33175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7553 (m-40) cc_final: 0.7255 (m-40) REVERT: B 69 TRP cc_start: 0.5297 (t60) cc_final: 0.2849 (t60) REVERT: B 104 MET cc_start: 0.8332 (tpp) cc_final: 0.7717 (tpp) REVERT: B 161 MET cc_start: 0.8301 (tpp) cc_final: 0.8048 (tpt) REVERT: B 175 LEU cc_start: 0.9106 (mt) cc_final: 0.8867 (mp) REVERT: B 198 THR cc_start: 0.8643 (p) cc_final: 0.8275 (t) REVERT: B 287 GLN cc_start: 0.8428 (tt0) cc_final: 0.7965 (tt0) REVERT: B 359 ILE cc_start: 0.8643 (mt) cc_final: 0.8382 (mm) REVERT: B 434 MET cc_start: 0.9011 (ttp) cc_final: 0.8659 (ttp) REVERT: B 492 GLU cc_start: 0.8398 (mp0) cc_final: 0.8013 (mm-30) REVERT: C 494 LEU cc_start: 0.9130 (pp) cc_final: 0.8595 (pp) REVERT: D 591 GLN cc_start: 0.8730 (tt0) cc_final: 0.8465 (tm-30) REVERT: D 637 ASN cc_start: 0.5519 (p0) cc_final: 0.5069 (t0) REVERT: D 638 TYR cc_start: 0.7439 (m-80) cc_final: 0.7094 (m-80) REVERT: E 647 GLU cc_start: 0.8266 (pp20) cc_final: 0.8022 (pp20) REVERT: F 534 SER cc_start: 0.8939 (m) cc_final: 0.8700 (m) REVERT: F 595 ILE cc_start: 0.8576 (tp) cc_final: 0.8198 (tp) REVERT: F 596 TRP cc_start: 0.8106 (m-10) cc_final: 0.6861 (m-10) REVERT: F 643 TYR cc_start: 0.7971 (m-10) cc_final: 0.7621 (m-80) REVERT: H 48 MET cc_start: 0.7626 (mmm) cc_final: 0.7340 (mmm) REVERT: H 77 ILE cc_start: 0.8767 (mm) cc_final: 0.8546 (mm) REVERT: H 80 MET cc_start: 0.8489 (tmm) cc_final: 0.8065 (tmm) REVERT: I 47 TRP cc_start: 0.8248 (t60) cc_final: 0.7466 (t60) REVERT: I 48 MET cc_start: 0.8530 (mmm) cc_final: 0.8230 (mmm) REVERT: I 80 MET cc_start: 0.8397 (tmm) cc_final: 0.6292 (tmm) REVERT: I 87 THR cc_start: 0.8789 (m) cc_final: 0.8507 (p) REVERT: I 98 ASP cc_start: 0.8195 (p0) cc_final: 0.7982 (p0) REVERT: K 45 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8274 (ptpt) REVERT: K 61 ARG cc_start: 0.6584 (ptm-80) cc_final: 0.6357 (ptm-80) REVERT: M 3 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7502 (tm-30) REVERT: M 22 CYS cc_start: 0.6013 (t) cc_final: 0.5177 (t) REVERT: M 33 TYR cc_start: 0.7099 (m-80) cc_final: 0.6289 (m-80) REVERT: M 51 ILE cc_start: 0.7844 (mt) cc_final: 0.7354 (tp) REVERT: M 92 CYS cc_start: 0.4655 (t) cc_final: 0.4274 (t) REVERT: N 100 MET cc_start: 0.8918 (mpp) cc_final: 0.8216 (mpp) REVERT: O 37 ILE cc_start: 0.8850 (mm) cc_final: 0.8567 (mm) REVERT: O 91 TYR cc_start: 0.7742 (m-10) cc_final: 0.7003 (m-10) REVERT: O 100 TYR cc_start: 0.8089 (m-10) cc_final: 0.7734 (m-80) REVERT: P 46 LEU cc_start: 0.7864 (pt) cc_final: 0.7604 (tt) REVERT: Q 66 ILE cc_start: 0.8578 (mm) cc_final: 0.8337 (mt) REVERT: Q 90 MET cc_start: 0.8175 (ttp) cc_final: 0.7883 (ttp) REVERT: R 47 LEU cc_start: 0.8534 (mp) cc_final: 0.8229 (mp) outliers start: 2 outliers final: 1 residues processed: 389 average time/residue: 0.3408 time to fit residues: 209.9243 Evaluate side-chains 300 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 117 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 9 optimal weight: 0.0050 chunk 258 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 155 optimal weight: 0.4980 chunk 236 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66CASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056584 restraints weight = 108312.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058094 restraints weight = 64488.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058973 restraints weight = 41633.504| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24580 Z= 0.135 Angle : 0.792 16.696 33560 Z= 0.364 Chirality : 0.050 0.418 3964 Planarity : 0.004 0.056 4106 Dihedral : 9.260 100.261 5165 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 2836 helix: -0.48 (0.27), residues: 380 sheet: -0.70 (0.18), residues: 799 loop : -1.53 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP N 47 HIS 0.008 0.001 HIS C 374 PHE 0.017 0.001 PHE C 383 TYR 0.029 0.001 TYR L 86 ARG 0.008 0.000 ARG Q 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 54) link_NAG-ASN : angle 3.43399 ( 162) link_ALPHA1-4 : bond 0.01966 ( 4) link_ALPHA1-4 : angle 4.20004 ( 12) link_BETA1-2 : bond 0.00112 ( 1) link_BETA1-2 : angle 2.92577 ( 3) link_BETA1-4 : bond 0.00723 ( 31) link_BETA1-4 : angle 3.24453 ( 93) link_ALPHA1-3 : bond 0.00787 ( 4) link_ALPHA1-3 : angle 3.21427 ( 12) hydrogen bonds : bond 0.03390 ( 728) hydrogen bonds : angle 6.16674 ( 1980) link_BETA1-6 : bond 0.00077 ( 1) link_BETA1-6 : angle 2.42830 ( 3) SS BOND : bond 0.00493 ( 44) SS BOND : angle 2.45155 ( 88) link_BETA1-3 : bond 0.00416 ( 4) link_BETA1-3 : angle 3.95638 ( 12) covalent geometry : bond 0.00303 (24437) covalent geometry : angle 0.71681 (33175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7856.27 seconds wall clock time: 137 minutes 39.52 seconds (8259.52 seconds total)