Starting phenix.real_space_refine on Fri Sep 19 06:29:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehm_48060/09_2025/9ehm_48060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehm_48060/09_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_48060/09_2025/9ehm_48060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehm_48060/09_2025/9ehm_48060.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehm_48060/09_2025/9ehm_48060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehm_48060/09_2025/9ehm_48060.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.84, per 1000 atoms: 0.20 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.87 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: 5.44 Time building geometry restraints manager: 2.73 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 607)) selection = (chain 'B' and (resid 36 through 58 or resid 63 through 136 or resid 152 through \ 185 or resid 189 through 607)) selection = (chain 'C' and (resid 36 through 58 or resid 63 through 136 or resid 152 through \ 458 or resid 464 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.940 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- 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 : 19.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (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 ARG 0.007 0.001 ARG F 588 TYR 0.024 0.001 TYR F 586 PHE 0.034 0.001 PHE D 522 TRP 0.055 0.002 TRP O 47 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00641 (24437) covalent geometry : angle 0.90660 (33175) SS BOND : bond 0.00491 ( 44) SS BOND : angle 2.45358 ( 88) hydrogen bonds : bond 0.25208 ( 728) hydrogen bonds : angle 10.65596 ( 1980) link_ALPHA1-3 : bond 0.04499 ( 4) link_ALPHA1-3 : angle 6.30421 ( 12) 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_BETA1-3 : bond 0.04538 ( 4) link_BETA1-3 : angle 4.80993 ( 12) link_BETA1-4 : bond 0.04586 ( 31) link_BETA1-4 : angle 7.20583 ( 93) link_BETA1-6 : bond 0.03794 ( 1) link_BETA1-6 : angle 3.53812 ( 3) link_NAG-ASN : bond 0.00719 ( 54) link_NAG-ASN : angle 3.28079 ( 162) *********************** 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 : 0.801 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: A 83 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6780 (mp0) REVERT: A 318 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) REVERT: A 390 LEU cc_start: 0.9265 (mt) cc_final: 0.8916 (mt) REVERT: A 396 ILE cc_start: 0.7951 (pt) cc_final: 0.7514 (mm) REVERT: B 69 TRP cc_start: 0.5475 (t60) cc_final: 0.3055 (t60) REVERT: B 161 MET cc_start: 0.8246 (tpp) cc_final: 0.7845 (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: 0.8254 (mm) REVERT: B 434 MET cc_start: 0.8871 (ttp) cc_final: 0.8399 (ttp) REVERT: B 481 SER cc_start: 0.8939 (m) cc_final: 0.8310 (t) REVERT: B 492 GLU cc_start: 0.8372 (mp0) cc_final: 0.7930 (mm-30) REVERT: C 104 MET cc_start: 0.7770 (ttp) cc_final: 0.7560 (ttp) REVERT: C 434 MET cc_start: 0.8498 (tmm) cc_final: 0.7913 (ttt) REVERT: D 595 ILE cc_start: 0.8662 (pt) cc_final: 0.8178 (mt) REVERT: D 601 LYS cc_start: 0.7474 (pttm) cc_final: 0.7066 (ptpp) REVERT: D 602 LEU cc_start: 0.7680 (mp) cc_final: 0.7405 (tt) REVERT: E 596 TRP cc_start: 0.8473 (m-10) cc_final: 0.8168 (m-10) REVERT: F 595 ILE cc_start: 0.8627 (tp) cc_final: 0.8303 (tp) REVERT: F 634 GLU cc_start: 0.7108 (pt0) cc_final: 0.6872 (pt0) REVERT: F 640 GLN cc_start: 0.8733 (tp40) cc_final: 0.8140 (pm20) REVERT: F 650 GLN cc_start: 0.8066 (mm110) cc_final: 0.7786 (mm-40) REVERT: H 73 THR cc_start: 0.8715 (m) cc_final: 0.8207 (m) REVERT: H 76 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7775 (mp0) REVERT: H 77 ILE cc_start: 0.8843 (mm) cc_final: 0.8641 (mm) REVERT: I 47 TRP cc_start: 0.8251 (t60) cc_final: 0.7884 (t60) REVERT: I 80 MET cc_start: 0.8499 (tmm) cc_final: 0.6054 (tmm) REVERT: K 27 VAL cc_start: 0.6990 (t) cc_final: 0.6789 (m) REVERT: K 36 TYR cc_start: 0.7907 (m-80) cc_final: 0.7606 (m-80) REVERT: K 49 TYR cc_start: 0.7253 (p90) cc_final: 0.6475 (p90) REVERT: L 49 TYR cc_start: 0.5846 (t80) cc_final: 0.5130 (t80) REVERT: L 86 TYR cc_start: 0.7864 (m-80) cc_final: 0.7474 (m-80) REVERT: L 96 VAL cc_start: 0.7206 (t) cc_final: 0.6689 (t) REVERT: M 51 ILE cc_start: 0.7707 (mt) cc_final: 0.7000 (tp) REVERT: M 72 ASP cc_start: 0.7103 (p0) cc_final: 0.5164 (p0) REVERT: M 78 LEU cc_start: 0.7536 (tp) cc_final: 0.7328 (tt) REVERT: N 46 GLU cc_start: 0.7871 (tt0) cc_final: 0.7613 (tt0) REVERT: N 100 TYR cc_start: 0.7670 (p90) cc_final: 0.7211 (p90) REVERT: O 5 GLN cc_start: 0.8981 (mm110) cc_final: 0.8770 (mt0) REVERT: O 78 LEU cc_start: 0.6483 (mm) cc_final: 0.6117 (tp) REVERT: O 90 TYR cc_start: 0.8162 (m-10) cc_final: 0.7789 (m-80) REVERT: O 91 TYR cc_start: 0.6920 (m-10) cc_final: 0.6562 (m-80) REVERT: O 100 GLU cc_start: 0.6273 (tt0) cc_final: 0.5954 (tt0) REVERT: P 39 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7772 (ptt-90) REVERT: P 46 LEU cc_start: 0.8047 (pt) cc_final: 0.7458 (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: 0.8140 (ttp) REVERT: Q 95 SER cc_start: 0.7666 (t) cc_final: 0.7396 (t) REVERT: Q 96 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6212 (t-100) REVERT: Q 98 PHE cc_start: 0.6610 (m-80) cc_final: 0.6373 (m-80) REVERT: R 66 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7608 (Cg_endo) REVERT: R 90 MET cc_start: 0.7375 (tmm) cc_final: 0.6895 (tmm) outliers start: 18 outliers final: 5 residues processed: 461 average time/residue: 0.1462 time to fit residues: 107.6483 Evaluate side-chains 315 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 309 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS I 6 GLN I 33 HIS ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.073617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057749 restraints weight = 107989.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059149 restraints weight = 62642.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060034 restraints weight = 44020.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060496 restraints weight = 35218.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060863 restraints weight = 31142.412| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24580 Z= 0.218 Angle : 0.988 20.704 33560 Z= 0.437 Chirality : 0.058 0.840 3964 Planarity : 0.005 0.063 4106 Dihedral : 16.271 107.192 5165 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.40 % Allowed : 5.93 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.15), residues: 2836 helix: -0.86 (0.25), residues: 401 sheet: -0.98 (0.18), residues: 817 loop : -1.76 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 273 TYR 0.028 0.002 TYR A 217 PHE 0.022 0.002 PHE C 383 TRP 0.032 0.002 TRP O 47 HIS 0.008 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00482 (24437) covalent geometry : angle 0.87029 (33175) SS BOND : bond 0.00515 ( 44) SS BOND : angle 2.35584 ( 88) hydrogen bonds : bond 0.04633 ( 728) hydrogen bonds : angle 7.86073 ( 1980) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 3.41655 ( 12) link_ALPHA1-4 : bond 0.01973 ( 4) link_ALPHA1-4 : angle 4.51887 ( 12) link_BETA1-2 : bond 0.00376 ( 1) link_BETA1-2 : angle 4.03476 ( 3) link_BETA1-3 : bond 0.00381 ( 4) link_BETA1-3 : angle 4.77074 ( 12) link_BETA1-4 : bond 0.01007 ( 31) link_BETA1-4 : angle 3.88020 ( 93) link_BETA1-6 : bond 0.00234 ( 1) link_BETA1-6 : angle 3.15244 ( 3) link_NAG-ASN : bond 0.00810 ( 54) link_NAG-ASN : angle 5.56334 ( 162) *********************** 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 432 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 422 time to evaluate : 0.799 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: A 318 TYR cc_start: 0.8546 (m-80) cc_final: 0.8340 (m-80) REVERT: A 396 ILE cc_start: 0.7824 (pt) cc_final: 0.7457 (mm) REVERT: A 443 ILE cc_start: 0.9169 (mm) cc_final: 0.8646 (tp) REVERT: B 161 MET cc_start: 0.8475 (tpp) cc_final: 0.7790 (tpt) REVERT: B 175 LEU cc_start: 0.9006 (mt) cc_final: 0.8617 (mp) REVERT: B 277 ILE cc_start: 0.7566 (pt) cc_final: 0.7121 (pt) REVERT: B 434 MET cc_start: 0.8950 (ttp) cc_final: 0.8729 (ttp) REVERT: B 492 GLU cc_start: 0.8350 (mp0) cc_final: 0.8025 (mm-30) REVERT: C 434 MET cc_start: 0.8600 (tmm) cc_final: 0.8056 (ttt) REVERT: D 601 LYS cc_start: 0.7373 (pttm) cc_final: 0.6911 (ptpp) REVERT: D 602 LEU cc_start: 0.7811 (mp) cc_final: 0.7410 (tt) REVERT: D 637 ASN cc_start: 0.5985 (p0) cc_final: 0.5603 (t0) REVERT: F 640 GLN cc_start: 0.8841 (tp40) cc_final: 0.8238 (pm20) REVERT: H 80 MET cc_start: 0.8925 (tmm) cc_final: 0.8612 (tmm) REVERT: I 47 TRP cc_start: 0.8406 (t60) cc_final: 0.7487 (t60) REVERT: I 62 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8693 (ptmm) REVERT: I 80 MET cc_start: 0.8532 (tmm) cc_final: 0.6126 (tmm) REVERT: I 100 MET cc_start: 0.8779 (ptp) cc_final: 0.8196 (ptp) REVERT: K 75 ILE cc_start: 0.7991 (mm) cc_final: 0.7417 (tp) REVERT: L 51 VAL cc_start: 0.7440 (p) cc_final: 0.7213 (p) REVERT: L 86 TYR cc_start: 0.8350 (m-80) cc_final: 0.7945 (m-10) REVERT: M 5 GLN cc_start: 0.6680 (pp30) cc_final: 0.6191 (pp30) REVERT: M 37 ILE cc_start: 0.7901 (tp) cc_final: 0.7683 (tp) REVERT: M 51 ILE cc_start: 0.7480 (mt) cc_final: 0.7039 (tp) REVERT: M 100 TYR cc_start: 0.7369 (m-80) cc_final: 0.7122 (m-80) REVERT: N 46 GLU cc_start: 0.8148 (tt0) cc_final: 0.7858 (tt0) REVERT: O 5 GLN cc_start: 0.8952 (mm110) cc_final: 0.8693 (mt0) REVERT: O 51 ILE cc_start: 0.7267 (mm) cc_final: 0.6493 (tt) REVERT: O 78 LEU cc_start: 0.6380 (mm) cc_final: 0.6016 (tp) REVERT: O 91 TYR cc_start: 0.7095 (m-10) cc_final: 0.6624 (m-10) REVERT: Q 53 ASP cc_start: 0.8961 (t0) cc_final: 0.8714 (t0) REVERT: Q 90 MET cc_start: 0.8409 (ttp) cc_final: 0.8209 (ttp) REVERT: R 66 PRO cc_start: 0.7951 (Cg_exo) cc_final: 0.7711 (Cg_endo) outliers start: 10 outliers final: 3 residues processed: 431 average time/residue: 0.1474 time to fit residues: 99.7949 Evaluate side-chains 293 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 90 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 168 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 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** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN 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 = 0.071003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055685 restraints weight = 108537.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056913 restraints weight = 62326.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057823 restraints weight = 40995.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057844 restraints weight = 37507.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057799 restraints weight = 32342.955| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 24580 Z= 0.252 Angle : 0.958 19.220 33560 Z= 0.429 Chirality : 0.056 0.457 3964 Planarity : 0.005 0.051 4106 Dihedral : 13.683 111.844 5165 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.15), residues: 2836 helix: -1.09 (0.25), residues: 404 sheet: -0.97 (0.18), residues: 830 loop : -1.76 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 39 TYR 0.044 0.002 TYR C 217 PHE 0.028 0.002 PHE B 383 TRP 0.038 0.003 TRP O 47 HIS 0.011 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00561 (24437) covalent geometry : angle 0.85497 (33175) SS BOND : bond 0.00595 ( 44) SS BOND : angle 2.48344 ( 88) hydrogen bonds : bond 0.04605 ( 728) hydrogen bonds : angle 7.37482 ( 1980) link_ALPHA1-3 : bond 0.00804 ( 4) link_ALPHA1-3 : angle 3.31123 ( 12) link_ALPHA1-4 : bond 0.02089 ( 4) link_ALPHA1-4 : angle 5.33925 ( 12) link_BETA1-2 : bond 0.00431 ( 1) link_BETA1-2 : angle 4.31526 ( 3) link_BETA1-3 : bond 0.00333 ( 4) link_BETA1-3 : angle 5.01527 ( 12) link_BETA1-4 : bond 0.00982 ( 31) link_BETA1-4 : angle 3.65340 ( 93) link_BETA1-6 : bond 0.00586 ( 1) link_BETA1-6 : angle 2.00900 ( 3) link_NAG-ASN : bond 0.00788 ( 54) link_NAG-ASN : angle 4.90671 ( 162) *********************** 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 394 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 391 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.8511 (m-80) cc_final: 0.8236 (m-80) REVERT: A 443 ILE cc_start: 0.9226 (mm) cc_final: 0.8629 (tp) REVERT: B 69 TRP cc_start: 0.5143 (t60) cc_final: 0.3498 (t60) REVERT: B 161 MET cc_start: 0.8492 (tpp) cc_final: 0.7791 (tpt) REVERT: B 175 LEU cc_start: 0.9047 (mt) cc_final: 0.8722 (mp) REVERT: B 434 MET cc_start: 0.9029 (ttp) cc_final: 0.8707 (ttp) REVERT: B 492 GLU cc_start: 0.8420 (mp0) cc_final: 0.7899 (mm-30) REVERT: C 161 MET cc_start: 0.8245 (tpp) cc_final: 0.7704 (tpt) REVERT: C 494 LEU cc_start: 0.9110 (pp) cc_final: 0.8678 (pp) REVERT: D 575 GLN cc_start: 0.8062 (tt0) cc_final: 0.7821 (tm-30) REVERT: D 637 ASN cc_start: 0.6067 (p0) cc_final: 0.5737 (t0) REVERT: D 655 LYS cc_start: 0.7816 (mttt) cc_final: 0.7353 (mtpt) REVERT: F 596 TRP cc_start: 0.8583 (m-10) cc_final: 0.8014 (m-10) REVERT: F 619 LEU cc_start: 0.8095 (tt) cc_final: 0.7751 (tp) REVERT: F 643 TYR cc_start: 0.8081 (m-10) cc_final: 0.7739 (m-10) REVERT: H 77 ILE cc_start: 0.8850 (mm) cc_final: 0.8611 (mm) REVERT: H 100 MET cc_start: 0.8327 (ptt) cc_final: 0.8083 (ptt) REVERT: I 34 MET cc_start: 0.8759 (tpp) cc_final: 0.8503 (tpp) REVERT: I 47 TRP cc_start: 0.8533 (t60) cc_final: 0.7793 (t60) REVERT: I 80 MET cc_start: 0.8465 (tmm) cc_final: 0.6089 (tmm) REVERT: I 100 MET cc_start: 0.8891 (ptp) cc_final: 0.8312 (ptp) REVERT: M 51 ILE cc_start: 0.7701 (mt) cc_final: 0.7289 (tp) REVERT: N 51 ILE cc_start: 0.7308 (tp) cc_final: 0.6965 (tp) REVERT: N 100 MET cc_start: 0.8928 (mpp) cc_final: 0.8213 (mpp) REVERT: O 78 LEU cc_start: 0.6323 (mm) cc_final: 0.5796 (tp) REVERT: O 105 LYS cc_start: 0.7741 (tppt) cc_final: 0.7404 (mtmm) REVERT: P 46 LEU cc_start: 0.8084 (pt) cc_final: 0.7559 (tt) REVERT: Q 53 ASP cc_start: 0.8997 (t0) cc_final: 0.8733 (t0) REVERT: Q 85 ASP cc_start: 0.8221 (m-30) cc_final: 0.7984 (m-30) REVERT: Q 90 MET cc_start: 0.8143 (ttp) cc_final: 0.7892 (ttp) REVERT: R 90 MET cc_start: 0.7143 (tmm) cc_final: 0.6692 (tmm) outliers start: 3 outliers final: 1 residues processed: 392 average time/residue: 0.1441 time to fit residues: 88.9835 Evaluate side-chains 287 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 108 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 43 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054880 restraints weight = 108526.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056250 restraints weight = 62392.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057058 restraints weight = 43840.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057595 restraints weight = 35487.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057865 restraints weight = 31001.150| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24580 Z= 0.208 Angle : 0.874 17.547 33560 Z= 0.395 Chirality : 0.053 0.455 3964 Planarity : 0.005 0.065 4106 Dihedral : 12.373 104.562 5165 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.15), residues: 2836 helix: -0.95 (0.25), residues: 398 sheet: -0.99 (0.18), residues: 825 loop : -1.76 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 588 TYR 0.026 0.002 TYR K 49 PHE 0.025 0.002 PHE B 383 TRP 0.064 0.002 TRP N 47 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00462 (24437) covalent geometry : angle 0.78091 (33175) SS BOND : bond 0.00942 ( 44) SS BOND : angle 2.40053 ( 88) hydrogen bonds : bond 0.03911 ( 728) hydrogen bonds : angle 7.02899 ( 1980) link_ALPHA1-3 : bond 0.00781 ( 4) link_ALPHA1-3 : angle 3.35337 ( 12) link_ALPHA1-4 : bond 0.01972 ( 4) link_ALPHA1-4 : angle 4.11441 ( 12) link_BETA1-2 : bond 0.00239 ( 1) link_BETA1-2 : angle 4.27029 ( 3) link_BETA1-3 : bond 0.00271 ( 4) link_BETA1-3 : angle 4.88741 ( 12) link_BETA1-4 : bond 0.00878 ( 31) link_BETA1-4 : angle 3.51738 ( 93) link_BETA1-6 : bond 0.00288 ( 1) link_BETA1-6 : angle 2.41063 ( 3) link_NAG-ASN : bond 0.00668 ( 54) link_NAG-ASN : angle 4.35292 ( 162) *********************** 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 383 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7751 (m-40) cc_final: 0.7497 (m-40) REVERT: A 318 TYR cc_start: 0.8656 (m-80) cc_final: 0.8052 (m-80) REVERT: A 396 ILE cc_start: 0.7947 (pt) cc_final: 0.7587 (mm) REVERT: B 69 TRP cc_start: 0.5170 (t60) cc_final: 0.2938 (t60) REVERT: B 161 MET cc_start: 0.8486 (tpp) cc_final: 0.7896 (tpt) REVERT: B 175 LEU cc_start: 0.9110 (mt) cc_final: 0.8803 (mp) REVERT: B 434 MET cc_start: 0.9017 (ttp) cc_final: 0.8755 (ttp) REVERT: B 492 GLU cc_start: 0.8392 (mp0) cc_final: 0.7908 (mm-30) REVERT: D 591 GLN cc_start: 0.8794 (tt0) cc_final: 0.8080 (tp40) REVERT: D 637 ASN cc_start: 0.5785 (p0) cc_final: 0.5483 (t0) REVERT: F 534 SER cc_start: 0.8983 (m) cc_final: 0.8736 (m) REVERT: F 595 ILE cc_start: 0.8619 (tp) cc_final: 0.8396 (tp) REVERT: F 619 LEU cc_start: 0.8039 (tt) cc_final: 0.7795 (tp) REVERT: H 43 GLN cc_start: 0.8527 (mp10) cc_final: 0.8307 (mp10) REVERT: H 97 PHE cc_start: 0.8044 (m-80) cc_final: 0.7666 (m-80) REVERT: I 34 MET cc_start: 0.8744 (tpp) cc_final: 0.8446 (tpp) REVERT: I 47 TRP cc_start: 0.8526 (t60) cc_final: 0.7811 (t60) REVERT: I 80 MET cc_start: 0.8356 (tmm) cc_final: 0.6092 (tmm) REVERT: I 100 MET cc_start: 0.8885 (ptp) cc_final: 0.8231 (ptp) REVERT: M 51 ILE cc_start: 0.7913 (mt) cc_final: 0.7458 (tp) REVERT: N 51 ILE cc_start: 0.7131 (tp) cc_final: 0.6826 (tp) REVERT: N 100 MET cc_start: 0.8839 (mpp) cc_final: 0.8024 (mpp) REVERT: O 22 CYS cc_start: 0.5487 (t) cc_final: 0.4491 (t) REVERT: O 78 LEU cc_start: 0.6548 (mm) cc_final: 0.6212 (tp) REVERT: Q 53 ASP cc_start: 0.8926 (t0) cc_final: 0.8718 (t0) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1351 time to fit residues: 83.0227 Evaluate side-chains 275 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 41 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 HIS ** 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 = 0.3459 r_free = 0.3459 target = 0.070663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055061 restraints weight = 108305.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056409 restraints weight = 62476.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057247 restraints weight = 43893.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057755 restraints weight = 35262.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058011 restraints weight = 30919.030| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24580 Z= 0.172 Angle : 0.851 17.136 33560 Z= 0.384 Chirality : 0.053 0.443 3964 Planarity : 0.004 0.051 4106 Dihedral : 11.767 105.912 5165 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.15), residues: 2836 helix: -0.90 (0.25), residues: 392 sheet: -0.97 (0.18), residues: 831 loop : -1.71 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 61 TYR 0.020 0.002 TYR C 217 PHE 0.022 0.002 PHE C 383 TRP 0.043 0.002 TRP O 47 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00390 (24437) covalent geometry : angle 0.76141 (33175) SS BOND : bond 0.00507 ( 44) SS BOND : angle 2.37622 ( 88) hydrogen bonds : bond 0.03688 ( 728) hydrogen bonds : angle 6.83703 ( 1980) link_ALPHA1-3 : bond 0.00788 ( 4) link_ALPHA1-3 : angle 3.32430 ( 12) link_ALPHA1-4 : bond 0.01879 ( 4) link_ALPHA1-4 : angle 3.94848 ( 12) link_BETA1-2 : bond 0.00141 ( 1) link_BETA1-2 : angle 3.71819 ( 3) link_BETA1-3 : bond 0.00255 ( 4) link_BETA1-3 : angle 4.72922 ( 12) link_BETA1-4 : bond 0.00763 ( 31) link_BETA1-4 : angle 3.43225 ( 93) link_BETA1-6 : bond 0.00342 ( 1) link_BETA1-6 : angle 2.47146 ( 3) link_NAG-ASN : bond 0.00555 ( 54) link_NAG-ASN : angle 4.17424 ( 162) *********************** 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 376 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7739 (m-40) cc_final: 0.7493 (m-40) REVERT: A 271 MET cc_start: 0.8230 (tpt) cc_final: 0.7908 (tmm) REVERT: A 318 TYR cc_start: 0.8635 (m-80) cc_final: 0.7949 (m-80) REVERT: A 396 ILE cc_start: 0.7935 (pt) cc_final: 0.7582 (mm) REVERT: A 443 ILE cc_start: 0.9111 (mm) cc_final: 0.8747 (tp) REVERT: B 69 TRP cc_start: 0.5279 (t60) cc_final: 0.3011 (t60) REVERT: B 161 MET cc_start: 0.8488 (tpp) cc_final: 0.7922 (tpt) REVERT: B 175 LEU cc_start: 0.9041 (mt) cc_final: 0.8797 (mp) REVERT: B 434 MET cc_start: 0.9037 (ttp) cc_final: 0.8763 (ttp) REVERT: B 492 GLU cc_start: 0.8407 (mp0) cc_final: 0.8057 (mm-30) REVERT: D 632 ASP cc_start: 0.7599 (p0) cc_final: 0.7126 (t70) REVERT: D 637 ASN cc_start: 0.5791 (p0) cc_final: 0.5444 (t0) REVERT: F 534 SER cc_start: 0.8897 (m) cc_final: 0.8645 (m) REVERT: F 612 SER cc_start: 0.7466 (m) cc_final: 0.7263 (p) REVERT: H 77 ILE cc_start: 0.8945 (mm) cc_final: 0.8707 (mm) REVERT: H 97 PHE cc_start: 0.8007 (m-80) cc_final: 0.7124 (m-80) REVERT: I 34 MET cc_start: 0.8736 (tpp) cc_final: 0.8395 (tpp) REVERT: I 47 TRP cc_start: 0.8559 (t60) cc_final: 0.8000 (t60) REVERT: I 48 MET cc_start: 0.8679 (mmm) cc_final: 0.8428 (mmm) REVERT: I 80 MET cc_start: 0.8348 (tmm) cc_final: 0.6131 (tmm) REVERT: I 100 MET cc_start: 0.8866 (ptp) cc_final: 0.8211 (ptp) REVERT: K 49 TYR cc_start: 0.8213 (p90) cc_final: 0.7974 (p90) REVERT: M 33 TYR cc_start: 0.6924 (m-80) cc_final: 0.6687 (m-80) REVERT: M 51 ILE cc_start: 0.7756 (mt) cc_final: 0.7382 (tp) REVERT: N 51 ILE cc_start: 0.7070 (tp) cc_final: 0.6747 (tp) REVERT: N 100 MET cc_start: 0.8959 (mpp) cc_final: 0.8217 (mpp) REVERT: O 13 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8642 (mtmm) REVERT: Q 53 ASP cc_start: 0.8952 (t0) cc_final: 0.8704 (t0) REVERT: Q 85 ASP cc_start: 0.8270 (m-30) cc_final: 0.7987 (m-30) REVERT: Q 90 MET cc_start: 0.8362 (ttp) cc_final: 0.8074 (ttt) REVERT: R 47 LEU cc_start: 0.8594 (mp) cc_final: 0.8383 (mp) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1336 time to fit residues: 80.8601 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 72 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 195 ASN B 478 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** F 658 GLN ** H 6 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** ** K 39 HIS ** 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** N 1 GLN N 99 GLN O 99 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.069465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053761 restraints weight = 109457.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055064 restraints weight = 64169.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055866 restraints weight = 45575.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056336 restraints weight = 36895.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056658 restraints weight = 32638.423| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24580 Z= 0.220 Angle : 0.880 17.905 33560 Z= 0.398 Chirality : 0.053 0.450 3964 Planarity : 0.004 0.063 4106 Dihedral : 11.541 102.361 5165 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2836 helix: -0.83 (0.26), residues: 386 sheet: -0.99 (0.18), residues: 817 loop : -1.73 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 54 TYR 0.028 0.002 TYR L 49 PHE 0.027 0.002 PHE C 383 TRP 0.044 0.002 TRP O 47 HIS 0.010 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00496 (24437) covalent geometry : angle 0.78863 (33175) SS BOND : bond 0.00630 ( 44) SS BOND : angle 2.52221 ( 88) hydrogen bonds : bond 0.03865 ( 728) hydrogen bonds : angle 6.79421 ( 1980) link_ALPHA1-3 : bond 0.00814 ( 4) link_ALPHA1-3 : angle 3.37621 ( 12) link_ALPHA1-4 : bond 0.01945 ( 4) link_ALPHA1-4 : angle 4.02359 ( 12) link_BETA1-2 : bond 0.00073 ( 1) link_BETA1-2 : angle 3.78167 ( 3) link_BETA1-3 : bond 0.00417 ( 4) link_BETA1-3 : angle 4.34559 ( 12) link_BETA1-4 : bond 0.00805 ( 31) link_BETA1-4 : angle 3.45074 ( 93) link_BETA1-6 : bond 0.00181 ( 1) link_BETA1-6 : angle 2.39598 ( 3) link_NAG-ASN : bond 0.00571 ( 54) link_NAG-ASN : angle 4.36354 ( 162) *********************** 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 378 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7718 (m-40) cc_final: 0.7461 (m-40) REVERT: A 318 TYR cc_start: 0.8597 (m-80) cc_final: 0.7930 (m-80) REVERT: A 396 ILE cc_start: 0.7825 (pt) cc_final: 0.7404 (mm) REVERT: A 443 ILE cc_start: 0.9076 (mm) cc_final: 0.8812 (tp) REVERT: B 69 TRP cc_start: 0.5433 (t60) cc_final: 0.3101 (t60) REVERT: B 161 MET cc_start: 0.8479 (tpp) cc_final: 0.7868 (tpt) REVERT: B 434 MET cc_start: 0.9035 (ttp) cc_final: 0.8764 (ttp) REVERT: B 492 GLU cc_start: 0.8399 (mp0) cc_final: 0.7980 (mm-30) REVERT: C 309 ILE cc_start: 0.8752 (tp) cc_final: 0.8472 (mt) REVERT: C 382 PHE cc_start: 0.7749 (m-80) cc_final: 0.7534 (m-10) REVERT: D 632 ASP cc_start: 0.7448 (p0) cc_final: 0.6847 (t70) REVERT: D 637 ASN cc_start: 0.5929 (p0) cc_final: 0.5464 (t0) REVERT: F 534 SER cc_start: 0.9036 (m) cc_final: 0.8827 (m) REVERT: F 595 ILE cc_start: 0.8622 (tp) cc_final: 0.8192 (tp) REVERT: H 77 ILE cc_start: 0.8900 (mm) cc_final: 0.8573 (mm) REVERT: I 34 MET cc_start: 0.8764 (tpp) cc_final: 0.8391 (tpp) REVERT: I 47 TRP cc_start: 0.8649 (t60) cc_final: 0.7686 (t60) REVERT: I 80 MET cc_start: 0.8320 (tmm) cc_final: 0.6145 (tmm) REVERT: K 49 TYR cc_start: 0.8254 (p90) cc_final: 0.8021 (p90) REVERT: K 61 ARG cc_start: 0.6495 (ptm-80) cc_final: 0.6269 (ptm-80) REVERT: M 33 TYR cc_start: 0.7067 (m-80) cc_final: 0.6742 (m-80) REVERT: M 51 ILE cc_start: 0.7792 (mt) cc_final: 0.7261 (tp) REVERT: N 46 GLU cc_start: 0.8188 (tt0) cc_final: 0.7896 (tt0) REVERT: N 51 ILE cc_start: 0.7078 (tp) cc_final: 0.6784 (tp) REVERT: N 100 MET cc_start: 0.8869 (mpp) cc_final: 0.7993 (mpp) REVERT: O 13 LYS cc_start: 0.8904 (ptpp) cc_final: 0.8607 (mtmm) REVERT: O 47 TRP cc_start: 0.4823 (p90) cc_final: 0.4597 (p90) REVERT: P 46 LEU cc_start: 0.8014 (pt) cc_final: 0.7577 (tt) REVERT: Q 53 ASP cc_start: 0.8839 (t0) cc_final: 0.8615 (t0) REVERT: Q 85 ASP cc_start: 0.8296 (m-30) cc_final: 0.8031 (m-30) REVERT: Q 90 MET cc_start: 0.8375 (ttp) cc_final: 0.8049 (ttt) REVERT: R 47 LEU cc_start: 0.8690 (mp) cc_final: 0.8399 (mp) REVERT: R 90 MET cc_start: 0.7447 (tmm) cc_final: 0.7113 (ttp) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.1335 time to fit residues: 81.4935 Evaluate side-chains 285 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 259 optimal weight: 0.0030 chunk 19 optimal weight: 0.0870 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** H 6 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** ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 60 ASN M 5 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055856 restraints weight = 107863.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057457 restraints weight = 64836.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057781 restraints weight = 42519.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058050 restraints weight = 38850.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058068 restraints weight = 35192.075| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24580 Z= 0.134 Angle : 0.825 17.064 33560 Z= 0.372 Chirality : 0.052 0.418 3964 Planarity : 0.004 0.050 4106 Dihedral : 10.702 102.778 5165 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.15), residues: 2836 helix: -0.75 (0.26), residues: 383 sheet: -0.86 (0.18), residues: 806 loop : -1.65 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 588 TYR 0.023 0.001 TYR F 586 PHE 0.017 0.001 PHE C 383 TRP 0.042 0.002 TRP N 47 HIS 0.006 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00301 (24437) covalent geometry : angle 0.74191 (33175) SS BOND : bond 0.00476 ( 44) SS BOND : angle 2.32360 ( 88) hydrogen bonds : bond 0.03516 ( 728) hydrogen bonds : angle 6.66180 ( 1980) link_ALPHA1-3 : bond 0.00832 ( 4) link_ALPHA1-3 : angle 3.37982 ( 12) link_ALPHA1-4 : bond 0.02101 ( 4) link_ALPHA1-4 : angle 4.07165 ( 12) link_BETA1-2 : bond 0.00212 ( 1) link_BETA1-2 : angle 3.31545 ( 3) link_BETA1-3 : bond 0.00387 ( 4) link_BETA1-3 : angle 4.53725 ( 12) link_BETA1-4 : bond 0.00801 ( 31) link_BETA1-4 : angle 3.36053 ( 93) link_BETA1-6 : bond 0.00302 ( 1) link_BETA1-6 : angle 2.64387 ( 3) link_NAG-ASN : bond 0.00492 ( 54) link_NAG-ASN : angle 3.87611 ( 162) *********************** 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 408 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.881 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: 0.7563 (m-40) cc_final: 0.7264 (m-40) REVERT: A 318 TYR cc_start: 0.8532 (m-80) cc_final: 0.7850 (m-80) REVERT: A 396 ILE cc_start: 0.7866 (pt) cc_final: 0.7498 (mm) REVERT: B 69 TRP cc_start: 0.5245 (t60) cc_final: 0.2920 (t60) REVERT: B 161 MET cc_start: 0.8360 (tpp) cc_final: 0.7985 (tpt) REVERT: B 175 LEU cc_start: 0.9102 (mt) cc_final: 0.8814 (mp) REVERT: B 359 ILE cc_start: 0.8691 (mt) cc_final: 0.8475 (mm) REVERT: B 434 MET cc_start: 0.9056 (ttp) cc_final: 0.8762 (ttp) REVERT: B 492 GLU cc_start: 0.8388 (mp0) cc_final: 0.8078 (mm-30) REVERT: D 606 THR cc_start: 0.8429 (t) cc_final: 0.8197 (m) REVERT: D 632 ASP cc_start: 0.7643 (p0) cc_final: 0.7000 (t70) REVERT: D 637 ASN cc_start: 0.5902 (p0) cc_final: 0.5476 (t0) REVERT: E 530 MET cc_start: 0.7345 (mtm) cc_final: 0.7004 (mtm) REVERT: F 534 SER cc_start: 0.8968 (m) cc_final: 0.8713 (m) REVERT: F 538 THR cc_start: 0.8101 (m) cc_final: 0.7834 (t) REVERT: F 595 ILE cc_start: 0.8708 (tp) cc_final: 0.8369 (tp) REVERT: H 97 PHE cc_start: 0.7935 (m-80) cc_final: 0.6979 (m-80) REVERT: I 34 MET cc_start: 0.8771 (tpp) cc_final: 0.8366 (tpp) REVERT: I 47 TRP cc_start: 0.8376 (t60) cc_final: 0.7689 (t60) REVERT: I 48 MET cc_start: 0.8534 (mmm) cc_final: 0.8297 (mmm) REVERT: I 80 MET cc_start: 0.8301 (tmm) cc_final: 0.6079 (tmm) REVERT: K 42 LYS cc_start: 0.7253 (mmpt) cc_final: 0.6274 (tptp) REVERT: K 49 TYR cc_start: 0.8260 (p90) cc_final: 0.7998 (p90) REVERT: K 61 ARG cc_start: 0.6478 (ptm-80) cc_final: 0.6240 (ptm-80) REVERT: M 3 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7300 (tm-30) REVERT: M 33 TYR cc_start: 0.6941 (m-80) cc_final: 0.6520 (m-80) REVERT: M 51 ILE cc_start: 0.7615 (mt) cc_final: 0.7200 (tp) REVERT: N 46 GLU cc_start: 0.8096 (tt0) cc_final: 0.7782 (tt0) REVERT: N 51 ILE cc_start: 0.7248 (tp) cc_final: 0.6966 (tp) REVERT: N 77 GLN cc_start: 0.7642 (pm20) cc_final: 0.7416 (pm20) REVERT: N 100 MET cc_start: 0.8868 (mpp) cc_final: 0.8013 (mpp) REVERT: P 46 LEU cc_start: 0.7998 (pt) cc_final: 0.7568 (tt) REVERT: Q 66 ILE cc_start: 0.8677 (mm) cc_final: 0.8450 (mt) REVERT: Q 90 MET cc_start: 0.8397 (ttp) cc_final: 0.8096 (ttt) REVERT: R 47 LEU cc_start: 0.8629 (mp) cc_final: 0.8389 (mp) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.1384 time to fit residues: 90.3358 Evaluate side-chains 291 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 177 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 232 optimal weight: 0.0070 chunk 214 optimal weight: 7.9990 chunk 182 optimal weight: 0.0970 overall best weight: 0.8376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN F 577 GLN ** H 6 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** K 37 GLN ** 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** ** 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 = 0.3471 r_free = 0.3471 target = 0.071120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056229 restraints weight = 108417.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057208 restraints weight = 64335.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057609 restraints weight = 43847.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057961 restraints weight = 39868.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057931 restraints weight = 36547.184| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24580 Z= 0.138 Angle : 0.823 17.184 33560 Z= 0.373 Chirality : 0.051 0.422 3964 Planarity : 0.004 0.070 4106 Dihedral : 10.133 102.270 5165 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.04 % Allowed : 1.20 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.15), residues: 2836 helix: -0.71 (0.26), residues: 382 sheet: -0.78 (0.19), residues: 781 loop : -1.65 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 39 TYR 0.019 0.001 TYR F 586 PHE 0.027 0.002 PHE A 382 TRP 0.045 0.002 TRP O 47 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00309 (24437) covalent geometry : angle 0.73821 (33175) SS BOND : bond 0.00504 ( 44) SS BOND : angle 2.37354 ( 88) hydrogen bonds : bond 0.03495 ( 728) hydrogen bonds : angle 6.48695 ( 1980) link_ALPHA1-3 : bond 0.00817 ( 4) link_ALPHA1-3 : angle 3.35090 ( 12) link_ALPHA1-4 : bond 0.02109 ( 4) link_ALPHA1-4 : angle 4.17388 ( 12) link_BETA1-2 : bond 0.00063 ( 1) link_BETA1-2 : angle 3.21067 ( 3) link_BETA1-3 : bond 0.00438 ( 4) link_BETA1-3 : angle 4.17944 ( 12) link_BETA1-4 : bond 0.00763 ( 31) link_BETA1-4 : angle 3.44656 ( 93) link_BETA1-6 : bond 0.00032 ( 1) link_BETA1-6 : angle 2.49208 ( 3) link_NAG-ASN : bond 0.00470 ( 54) link_NAG-ASN : angle 3.87575 ( 162) *********************** 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 383 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 0.715 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: A 195 ASN cc_start: 0.7643 (m-40) cc_final: 0.7303 (m-40) REVERT: A 318 TYR cc_start: 0.8541 (m-80) cc_final: 0.7885 (m-80) REVERT: A 396 ILE cc_start: 0.7981 (pt) cc_final: 0.7697 (mm) REVERT: B 69 TRP cc_start: 0.5306 (t60) cc_final: 0.2954 (t60) REVERT: B 161 MET cc_start: 0.8370 (tpp) cc_final: 0.8148 (tpt) REVERT: B 175 LEU cc_start: 0.9058 (mt) cc_final: 0.8829 (mp) REVERT: B 198 THR cc_start: 0.8638 (p) cc_final: 0.8323 (t) REVERT: B 359 ILE cc_start: 0.8743 (mt) cc_final: 0.8508 (mm) REVERT: B 434 MET cc_start: 0.9065 (ttp) cc_final: 0.8732 (ttp) REVERT: B 492 GLU cc_start: 0.8403 (mp0) cc_final: 0.8052 (mm-30) REVERT: D 632 ASP cc_start: 0.7770 (p0) cc_final: 0.7159 (t70) REVERT: D 637 ASN cc_start: 0.5796 (p0) cc_final: 0.5416 (t0) REVERT: D 638 TYR cc_start: 0.7795 (m-80) cc_final: 0.7447 (m-80) REVERT: D 658 GLN cc_start: 0.7765 (pt0) cc_final: 0.7558 (pt0) REVERT: E 530 MET cc_start: 0.7440 (mtm) cc_final: 0.7094 (mtm) REVERT: F 534 SER cc_start: 0.8935 (m) cc_final: 0.8699 (m) REVERT: F 626 MET cc_start: 0.6329 (ttt) cc_final: 0.6111 (ttm) REVERT: H 76 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8489 (mt-10) REVERT: H 77 ILE cc_start: 0.8894 (mm) cc_final: 0.8656 (mm) REVERT: H 80 MET cc_start: 0.8479 (tmm) cc_final: 0.8063 (tmm) REVERT: H 97 PHE cc_start: 0.7925 (m-80) cc_final: 0.6987 (m-80) REVERT: I 34 MET cc_start: 0.8781 (tpp) cc_final: 0.8363 (tpp) REVERT: I 43 GLN cc_start: 0.6272 (pp30) cc_final: 0.5958 (pp30) REVERT: I 47 TRP cc_start: 0.8345 (t60) cc_final: 0.7507 (t60) REVERT: I 48 MET cc_start: 0.8497 (mmm) cc_final: 0.8246 (mmm) REVERT: I 80 MET cc_start: 0.8286 (tmm) cc_final: 0.6104 (tmm) REVERT: K 36 TYR cc_start: 0.8249 (m-10) cc_final: 0.7934 (m-10) REVERT: K 61 ARG cc_start: 0.6499 (ptm-80) cc_final: 0.6252 (ptm-80) REVERT: L 75 ILE cc_start: 0.7233 (tt) cc_final: 0.6974 (tt) REVERT: M 33 TYR cc_start: 0.7026 (m-80) cc_final: 0.6360 (m-80) REVERT: M 50 TYR cc_start: 0.6537 (p90) cc_final: 0.6336 (p90) REVERT: M 51 ILE cc_start: 0.7611 (mt) cc_final: 0.7201 (tp) REVERT: N 46 GLU cc_start: 0.8189 (tt0) cc_final: 0.7737 (tt0) REVERT: N 100 MET cc_start: 0.8824 (mpp) cc_final: 0.8140 (mpp) REVERT: O 90 TYR cc_start: 0.8094 (m-10) cc_final: 0.7854 (m-10) REVERT: P 46 LEU cc_start: 0.7946 (pt) cc_final: 0.7543 (tt) REVERT: Q 66 ILE cc_start: 0.8649 (mm) cc_final: 0.8437 (mt) REVERT: Q 90 MET cc_start: 0.8430 (ttp) cc_final: 0.8085 (ttt) REVERT: R 47 LEU cc_start: 0.8677 (mp) cc_final: 0.8419 (mp) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.1355 time to fit residues: 83.6784 Evaluate side-chains 279 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 278 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 66 HIS B 195 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS L 37 GLN L 60 ASN ** M 60 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056365 restraints weight = 108836.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058027 restraints weight = 62655.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058306 restraints weight = 41762.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058578 restraints weight = 35582.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058650 restraints weight = 34296.664| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24580 Z= 0.134 Angle : 0.804 16.890 33560 Z= 0.366 Chirality : 0.051 0.425 3964 Planarity : 0.004 0.059 4106 Dihedral : 9.592 101.519 5165 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.08 % Allowed : 0.96 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.15), residues: 2836 helix: -0.72 (0.26), residues: 383 sheet: -0.85 (0.18), residues: 809 loop : -1.61 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 66 TYR 0.021 0.001 TYR L 49 PHE 0.020 0.001 PHE Q 62 TRP 0.042 0.002 TRP N 47 HIS 0.008 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00302 (24437) covalent geometry : angle 0.71992 (33175) SS BOND : bond 0.00463 ( 44) SS BOND : angle 2.64957 ( 88) hydrogen bonds : bond 0.03445 ( 728) hydrogen bonds : angle 6.39608 ( 1980) link_ALPHA1-3 : bond 0.00786 ( 4) link_ALPHA1-3 : angle 3.33981 ( 12) link_ALPHA1-4 : bond 0.02016 ( 4) link_ALPHA1-4 : angle 4.30218 ( 12) link_BETA1-2 : bond 0.00053 ( 1) link_BETA1-2 : angle 3.23006 ( 3) link_BETA1-3 : bond 0.00469 ( 4) link_BETA1-3 : angle 4.14139 ( 12) link_BETA1-4 : bond 0.00740 ( 31) link_BETA1-4 : angle 3.37913 ( 93) link_BETA1-6 : bond 0.00099 ( 1) link_BETA1-6 : angle 2.54019 ( 3) link_NAG-ASN : bond 0.00454 ( 54) link_NAG-ASN : angle 3.68488 ( 162) *********************** 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 382 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7571 (m-40) cc_final: 0.7264 (m-40) REVERT: A 318 TYR cc_start: 0.8279 (m-80) cc_final: 0.7902 (m-80) REVERT: A 396 ILE cc_start: 0.7894 (pt) cc_final: 0.7654 (mm) REVERT: B 69 TRP cc_start: 0.5373 (t60) cc_final: 0.2992 (t60) REVERT: B 175 LEU cc_start: 0.9059 (mt) cc_final: 0.8831 (mp) REVERT: B 198 THR cc_start: 0.8576 (p) cc_final: 0.8272 (t) REVERT: B 434 MET cc_start: 0.9035 (ttp) cc_final: 0.8697 (ttp) REVERT: B 492 GLU cc_start: 0.8411 (mp0) cc_final: 0.8048 (mm-30) REVERT: C 494 LEU cc_start: 0.9106 (pp) cc_final: 0.8646 (pp) REVERT: D 591 GLN cc_start: 0.8791 (tt0) cc_final: 0.8524 (tm-30) REVERT: D 637 ASN cc_start: 0.5714 (p0) cc_final: 0.5283 (t0) REVERT: D 638 TYR cc_start: 0.7601 (m-80) cc_final: 0.7332 (m-80) REVERT: D 658 GLN cc_start: 0.7763 (pt0) cc_final: 0.7552 (pt0) REVERT: E 530 MET cc_start: 0.7398 (mtm) cc_final: 0.7035 (mtm) REVERT: F 534 SER cc_start: 0.8939 (m) cc_final: 0.8720 (m) REVERT: F 643 TYR cc_start: 0.8062 (m-10) cc_final: 0.7793 (m-10) REVERT: H 77 ILE cc_start: 0.8879 (mm) cc_final: 0.8635 (mm) REVERT: H 80 MET cc_start: 0.8450 (tmm) cc_final: 0.8139 (tmm) REVERT: H 97 PHE cc_start: 0.7776 (m-80) cc_final: 0.6865 (m-80) REVERT: I 47 TRP cc_start: 0.8311 (t60) cc_final: 0.7472 (t60) REVERT: I 48 MET cc_start: 0.8478 (mmm) cc_final: 0.8239 (mmm) REVERT: I 80 MET cc_start: 0.8267 (tmm) cc_final: 0.6149 (tmm) REVERT: I 87 THR cc_start: 0.8866 (m) cc_final: 0.8558 (p) REVERT: K 61 ARG cc_start: 0.6528 (ptm-80) cc_final: 0.6082 (ptm160) REVERT: L 83 GLU cc_start: 0.7988 (tt0) cc_final: 0.7301 (tp30) REVERT: L 87 TYR cc_start: 0.7126 (m-80) cc_final: 0.6863 (m-80) REVERT: M 3 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7580 (tm-30) REVERT: M 33 TYR cc_start: 0.7140 (m-80) cc_final: 0.6389 (m-80) REVERT: M 50 TYR cc_start: 0.6609 (p90) cc_final: 0.6276 (p90) REVERT: M 51 ILE cc_start: 0.7579 (mt) cc_final: 0.7188 (tp) REVERT: N 46 GLU cc_start: 0.8083 (tt0) cc_final: 0.7685 (tt0) REVERT: N 77 GLN cc_start: 0.7322 (pm20) cc_final: 0.6964 (pm20) REVERT: N 100 MET cc_start: 0.8855 (mpp) cc_final: 0.8127 (mpp) REVERT: P 46 LEU cc_start: 0.7923 (pt) cc_final: 0.7600 (tt) REVERT: Q 66 ILE cc_start: 0.8547 (mm) cc_final: 0.8337 (mt) REVERT: R 47 LEU cc_start: 0.8687 (mp) cc_final: 0.8377 (mp) outliers start: 2 outliers final: 1 residues processed: 381 average time/residue: 0.1399 time to fit residues: 85.9380 Evaluate side-chains 288 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 239 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** H 6 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** K 37 GLN K 39 HIS L 37 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** 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 = 0.3485 r_free = 0.3485 target = 0.071677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056497 restraints weight = 109108.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058191 restraints weight = 63308.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058376 restraints weight = 41612.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058702 restraints weight = 37338.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058714 restraints weight = 34124.271| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24580 Z= 0.132 Angle : 0.801 16.886 33560 Z= 0.366 Chirality : 0.050 0.427 3964 Planarity : 0.004 0.054 4106 Dihedral : 9.314 101.294 5165 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 2836 helix: -0.58 (0.26), residues: 377 sheet: -0.74 (0.18), residues: 799 loop : -1.58 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 588 TYR 0.021 0.001 TYR L 49 PHE 0.019 0.001 PHE A 382 TRP 0.073 0.002 TRP O 47 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (24437) covalent geometry : angle 0.72059 (33175) SS BOND : bond 0.00579 ( 44) SS BOND : angle 2.64450 ( 88) hydrogen bonds : bond 0.03368 ( 728) hydrogen bonds : angle 6.29961 ( 1980) link_ALPHA1-3 : bond 0.00795 ( 4) link_ALPHA1-3 : angle 3.25871 ( 12) link_ALPHA1-4 : bond 0.02018 ( 4) link_ALPHA1-4 : angle 4.24139 ( 12) link_BETA1-2 : bond 0.00087 ( 1) link_BETA1-2 : angle 3.18970 ( 3) link_BETA1-3 : bond 0.00495 ( 4) link_BETA1-3 : angle 4.04643 ( 12) link_BETA1-4 : bond 0.00738 ( 31) link_BETA1-4 : angle 3.28929 ( 93) link_BETA1-6 : bond 0.00087 ( 1) link_BETA1-6 : angle 2.47831 ( 3) link_NAG-ASN : bond 0.00447 ( 54) link_NAG-ASN : angle 3.58416 ( 162) ********************** 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 375 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.973 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: 0.7520 (m-40) cc_final: 0.7181 (m-40) REVERT: A 318 TYR cc_start: 0.8250 (m-80) cc_final: 0.7899 (m-80) REVERT: A 396 ILE cc_start: 0.7882 (pt) cc_final: 0.7647 (mm) REVERT: B 69 TRP cc_start: 0.5348 (t60) cc_final: 0.2946 (t60) REVERT: B 175 LEU cc_start: 0.9060 (mt) cc_final: 0.8850 (mp) REVERT: B 198 THR cc_start: 0.8658 (p) cc_final: 0.8301 (t) REVERT: B 434 MET cc_start: 0.9033 (ttp) cc_final: 0.8712 (ttp) REVERT: B 492 GLU cc_start: 0.8409 (mp0) cc_final: 0.8058 (mm-30) REVERT: D 591 GLN cc_start: 0.8797 (tt0) cc_final: 0.8543 (tm-30) REVERT: D 637 ASN cc_start: 0.5647 (p0) cc_final: 0.5343 (t0) REVERT: D 638 TYR cc_start: 0.7628 (m-80) cc_final: 0.7257 (m-80) REVERT: F 534 SER cc_start: 0.8926 (m) cc_final: 0.8685 (m) REVERT: H 77 ILE cc_start: 0.8829 (mm) cc_final: 0.8573 (mm) REVERT: H 80 MET cc_start: 0.8462 (tmm) cc_final: 0.8150 (tmm) REVERT: H 81 GLU cc_start: 0.7776 (pp20) cc_final: 0.7549 (pp20) REVERT: H 97 PHE cc_start: 0.7796 (m-80) cc_final: 0.6804 (m-80) REVERT: I 47 TRP cc_start: 0.8251 (t60) cc_final: 0.7472 (t60) REVERT: I 48 MET cc_start: 0.8499 (mmm) cc_final: 0.8266 (mmm) REVERT: I 80 MET cc_start: 0.8267 (tmm) cc_final: 0.6207 (tmm) REVERT: I 87 THR cc_start: 0.8841 (m) cc_final: 0.8531 (p) REVERT: K 36 TYR cc_start: 0.8286 (m-10) cc_final: 0.7955 (m-10) REVERT: K 61 ARG cc_start: 0.6508 (ptm-80) cc_final: 0.6041 (ptm160) REVERT: L 37 GLN cc_start: 0.8155 (pt0) cc_final: 0.7357 (pt0) REVERT: L 47 MET cc_start: 0.6787 (mpp) cc_final: 0.6247 (mpp) REVERT: L 54 ARG cc_start: 0.7356 (ttt-90) cc_final: 0.6817 (mmm-85) REVERT: L 60 ASN cc_start: 0.8883 (t0) cc_final: 0.8683 (t0) REVERT: L 82 ASP cc_start: 0.7335 (m-30) cc_final: 0.7108 (m-30) REVERT: L 83 GLU cc_start: 0.8021 (tt0) cc_final: 0.7326 (tp30) REVERT: L 87 TYR cc_start: 0.7105 (m-80) cc_final: 0.6885 (m-80) REVERT: M 3 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7619 (tm-30) REVERT: M 33 TYR cc_start: 0.7162 (m-80) cc_final: 0.6621 (m-80) REVERT: M 47 TRP cc_start: 0.8180 (m-10) cc_final: 0.7929 (m-10) REVERT: M 50 TYR cc_start: 0.6622 (p90) cc_final: 0.6144 (p90) REVERT: M 51 ILE cc_start: 0.7662 (mt) cc_final: 0.7289 (tp) REVERT: N 46 GLU cc_start: 0.8091 (tt0) cc_final: 0.7685 (tt0) REVERT: N 77 GLN cc_start: 0.7105 (pm20) cc_final: 0.6873 (pm20) REVERT: N 100 MET cc_start: 0.8858 (mpp) cc_final: 0.8149 (mpp) REVERT: P 46 LEU cc_start: 0.7887 (pt) cc_final: 0.7559 (tt) REVERT: Q 66 ILE cc_start: 0.8542 (mm) cc_final: 0.8330 (mt) REVERT: R 47 LEU cc_start: 0.8515 (mp) cc_final: 0.8226 (mp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1283 time to fit residues: 78.1698 Evaluate side-chains 295 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 293 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 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** K 39 HIS L 37 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055315 restraints weight = 109028.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056378 restraints weight = 66084.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056677 restraints weight = 43586.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056939 restraints weight = 42206.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056975 restraints weight = 36785.558| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24580 Z= 0.171 Angle : 0.824 17.123 33560 Z= 0.381 Chirality : 0.050 0.406 3964 Planarity : 0.004 0.050 4106 Dihedral : 9.269 98.909 5165 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.15), residues: 2836 helix: -0.64 (0.26), residues: 380 sheet: -0.73 (0.19), residues: 800 loop : -1.59 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 54 TYR 0.026 0.002 TYR F 586 PHE 0.020 0.002 PHE C 383 TRP 0.048 0.002 TRP N 47 HIS 0.012 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (24437) covalent geometry : angle 0.74508 (33175) SS BOND : bond 0.00597 ( 44) SS BOND : angle 2.72234 ( 88) hydrogen bonds : bond 0.03628 ( 728) hydrogen bonds : angle 6.32610 ( 1980) link_ALPHA1-3 : bond 0.00770 ( 4) link_ALPHA1-3 : angle 3.25649 ( 12) link_ALPHA1-4 : bond 0.01901 ( 4) link_ALPHA1-4 : angle 4.27198 ( 12) link_BETA1-2 : bond 0.00248 ( 1) link_BETA1-2 : angle 3.13987 ( 3) link_BETA1-3 : bond 0.00490 ( 4) link_BETA1-3 : angle 3.64904 ( 12) link_BETA1-4 : bond 0.00722 ( 31) link_BETA1-4 : angle 3.25794 ( 93) link_BETA1-6 : bond 0.00091 ( 1) link_BETA1-6 : angle 2.38794 ( 3) link_NAG-ASN : bond 0.00480 ( 54) link_NAG-ASN : angle 3.64365 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.35 seconds wall clock time: 62 minutes 45.80 seconds (3765.80 seconds total)