Starting phenix.real_space_refine on Tue May 20 11:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl5_41362/05_2025/8tl5_41362.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 132 5.16 5 C 12372 2.51 5 N 3357 2.21 5 O 3969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19830 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 934 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 934 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 934 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.99, per 1000 atoms: 0.71 Number of scatterers: 19830 At special positions: 0 Unit cell: (156.33, 158.057, 132.146, 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 132 16.00 O 3969 8.00 N 3357 7.00 C 12372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 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 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 6.01 Conformation dependent library (CDL) restraints added in 2.5 seconds 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 19.1% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.150A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.884A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.352A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.243A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.604A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.422A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.149A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.873A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 521 through 527 removed outlier: 4.544A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.174A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.561A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.580A pdb=" N TYR D 643 " --> pdb=" O THR D 639 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.150A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.897A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.580A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.131A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.621A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.615A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.044A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.056A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.023A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.609A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.846A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.575A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.934A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.655A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.543A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.817A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.475A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.935A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 457 current: chain 'C' and resid 413 through 417 Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.575A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.919A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.499A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.924A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.459A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.193A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.651A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU G 33 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY G 96 " --> pdb=" O LEU G 100I" (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU G 100I" --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL G 98 " --> pdb=" O ARG G 100G" (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG G 100G" --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.628A pdb=" N VAL H 33 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLY I 10 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU I 33 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLY I 10 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY I 96 " --> pdb=" O LEU I 100I" (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU I 100I" --> pdb=" O GLY I 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL I 98 " --> pdb=" O ARG I 100G" (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG I 100G" --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.599A pdb=" N VAL J 33 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLY K 10 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU K 33 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLY K 10 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY K 96 " --> pdb=" O LEU K 100I" (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU K 100I" --> pdb=" O GLY K 96 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL K 98 " --> pdb=" O ARG K 100G" (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG K 100G" --> pdb=" O VAL K 98 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.670A pdb=" N VAL L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6312 1.35 - 1.47: 5063 1.47 - 1.59: 8662 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 20217 Sorted by residual: bond pdb=" CA ASN A 377 " pdb=" CB ASN A 377 " ideal model delta sigma weight residual 1.535 1.574 -0.038 2.09e-02 2.29e+03 3.37e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N GLU K 1 " pdb=" CA GLU K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 20212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 26112 1.36 - 2.72: 1018 2.72 - 4.08: 197 4.08 - 5.44: 86 5.44 - 6.80: 16 Bond angle restraints: 27429 Sorted by residual: angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.46 3.71 1.14e+00 7.69e-01 1.06e+01 angle pdb=" CA ASN B 607 " pdb=" CB ASN B 607 " pdb=" CG ASN B 607 " ideal model delta sigma weight residual 112.60 115.83 -3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" CA ASN F 637 " pdb=" CB ASN F 637 " pdb=" CG ASN F 637 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 120.89 -6.49 2.30e+00 1.89e-01 7.95e+00 angle pdb=" CA ASN B 637 " pdb=" CB ASN B 637 " pdb=" CG ASN B 637 " ideal model delta sigma weight residual 112.60 115.21 -2.61 1.00e+00 1.00e+00 6.82e+00 ... (remaining 27424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 11963 21.77 - 43.55: 992 43.55 - 65.32: 181 65.32 - 87.09: 60 87.09 - 108.87: 31 Dihedral angle restraints: 13227 sinusoidal: 6393 harmonic: 6834 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 1.51 -87.51 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 7.71 85.29 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -163.58 77.58 1 1.00e+01 1.00e-02 7.53e+01 ... (remaining 13224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2798 0.057 - 0.113: 402 0.113 - 0.170: 109 0.170 - 0.227: 3 0.227 - 0.283: 9 Chirality restraints: 3321 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3318 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " -0.205 9.50e-02 1.11e+02 9.23e-02 5.98e+00 pdb=" NE ARG A 444 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 75 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 76 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 167 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" CG ASP A 167 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP A 167 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 167 " 0.011 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 514 2.70 - 3.25: 17836 3.25 - 3.80: 29157 3.80 - 4.35: 37567 4.35 - 4.90: 65947 Nonbonded interactions: 151021 Sorted by model distance: nonbonded pdb=" OE1 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.153 3.040 nonbonded pdb=" O3 NAG o 1 " pdb=" O5 NAG o 2 " model vdw 2.159 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.164 3.040 nonbonded pdb=" O3 NAG T 1 " pdb=" O5 NAG T 2 " model vdw 2.168 3.040 nonbonded pdb=" OG SER I 70 " pdb=" OG SER I 79 " model vdw 2.171 3.040 ... (remaining 151016 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.570 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20346 Z= 0.212 Angle : 0.680 6.796 27774 Z= 0.318 Chirality : 0.048 0.283 3321 Planarity : 0.004 0.092 3402 Dihedral : 16.589 108.867 8697 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.14 % Allowed : 12.31 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2349 helix: 2.31 (0.29), residues: 390 sheet: 0.48 (0.19), residues: 753 loop : -0.29 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 103 HIS 0.003 0.001 HIS C 216 PHE 0.012 0.001 PHE D 519 TYR 0.016 0.001 TYR C 173 ARG 0.015 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 45) link_NAG-ASN : angle 1.82825 ( 135) link_BETA1-4 : bond 0.00457 ( 36) link_BETA1-4 : angle 1.06528 ( 108) link_ALPHA1-2 : bond 0.00365 ( 3) link_ALPHA1-2 : angle 1.66384 ( 9) link_ALPHA1-3 : bond 0.00487 ( 3) link_ALPHA1-3 : angle 1.45848 ( 9) hydrogen bonds : bond 0.11416 ( 704) hydrogen bonds : angle 4.96922 ( 1887) SS BOND : bond 0.00455 ( 42) SS BOND : angle 1.34424 ( 84) covalent geometry : bond 0.00442 (20217) covalent geometry : angle 0.66389 (27429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.8562 (mt) cc_final: 0.8292 (pt) REVERT: E 248 THR cc_start: 0.8888 (m) cc_final: 0.8578 (p) REVERT: F 606 THR cc_start: 0.8269 (p) cc_final: 0.8023 (p) REVERT: L 3 GLN cc_start: 0.6794 (pm20) cc_final: 0.6518 (pm20) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.3440 time to fit residues: 128.6293 Evaluate side-chains 230 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain J residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 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 94 ASN A 355 ASN B 625 ASN D 653 GLN E 330 HIS G 100FASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.178066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123112 restraints weight = 22610.966| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.51 r_work: 0.3033 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20346 Z= 0.157 Angle : 0.610 9.234 27774 Z= 0.299 Chirality : 0.045 0.231 3321 Planarity : 0.004 0.049 3402 Dihedral : 9.141 71.332 4344 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.55 % Allowed : 12.27 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2349 helix: 2.09 (0.29), residues: 393 sheet: 0.60 (0.20), residues: 732 loop : -0.31 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 623 HIS 0.008 0.001 HIS J 91 PHE 0.018 0.002 PHE A 383 TYR 0.015 0.001 TYR C 173 ARG 0.006 0.001 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 45) link_NAG-ASN : angle 2.14046 ( 135) link_BETA1-4 : bond 0.00638 ( 36) link_BETA1-4 : angle 1.38979 ( 108) link_ALPHA1-2 : bond 0.00578 ( 3) link_ALPHA1-2 : angle 1.81087 ( 9) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 2.21612 ( 9) hydrogen bonds : bond 0.04451 ( 704) hydrogen bonds : angle 4.45423 ( 1887) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.38807 ( 84) covalent geometry : bond 0.00370 (20217) covalent geometry : angle 0.58175 (27429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7871 (mm-30) REVERT: A 215 ILE cc_start: 0.8696 (mt) cc_final: 0.8463 (pt) REVERT: A 363 ASN cc_start: 0.8244 (m-40) cc_final: 0.7938 (m-40) REVERT: A 426 MET cc_start: 0.7515 (tpp) cc_final: 0.7222 (ttt) REVERT: A 457 ASP cc_start: 0.7835 (t0) cc_final: 0.7609 (t0) REVERT: B 653 GLN cc_start: 0.7370 (tt0) cc_final: 0.6863 (mt0) REVERT: C 347 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7724 (ttmt) REVERT: E 308 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8453 (mtt-85) REVERT: F 542 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8193 (mtm-85) REVERT: F 653 GLN cc_start: 0.7441 (tt0) cc_final: 0.6898 (mt0) REVERT: H 4 MET cc_start: 0.7751 (tpp) cc_final: 0.7217 (tpp) outliers start: 53 outliers final: 31 residues processed: 273 average time/residue: 0.3392 time to fit residues: 139.2162 Evaluate side-chains 260 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 625 ASN C 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.176234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120349 restraints weight = 22392.138| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.57 r_work: 0.2998 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20346 Z= 0.127 Angle : 0.548 9.764 27774 Z= 0.270 Chirality : 0.043 0.229 3321 Planarity : 0.004 0.047 3402 Dihedral : 7.086 57.552 4342 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.69 % Allowed : 12.89 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2349 helix: 2.46 (0.29), residues: 375 sheet: 0.66 (0.19), residues: 747 loop : -0.44 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 623 HIS 0.005 0.001 HIS J 91 PHE 0.016 0.001 PHE E 383 TYR 0.012 0.001 TYR E 173 ARG 0.011 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 45) link_NAG-ASN : angle 2.02607 ( 135) link_BETA1-4 : bond 0.00495 ( 36) link_BETA1-4 : angle 1.26140 ( 108) link_ALPHA1-2 : bond 0.00496 ( 3) link_ALPHA1-2 : angle 1.53694 ( 9) link_ALPHA1-3 : bond 0.01236 ( 3) link_ALPHA1-3 : angle 1.33085 ( 9) hydrogen bonds : bond 0.04022 ( 704) hydrogen bonds : angle 4.32848 ( 1887) SS BOND : bond 0.00441 ( 42) SS BOND : angle 1.17299 ( 84) covalent geometry : bond 0.00302 (20217) covalent geometry : angle 0.52138 (27429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8062 (mm-30) REVERT: A 215 ILE cc_start: 0.8612 (mt) cc_final: 0.8381 (pt) REVERT: A 457 ASP cc_start: 0.7758 (t0) cc_final: 0.7550 (t0) REVERT: B 612 SER cc_start: 0.8329 (m) cc_final: 0.8083 (t) REVERT: E 114 GLN cc_start: 0.8459 (mt0) cc_final: 0.7954 (tt0) REVERT: E 280 ASN cc_start: 0.8253 (p0) cc_final: 0.7765 (m-40) REVERT: E 308 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8414 (mtt-85) REVERT: F 653 GLN cc_start: 0.7426 (tt0) cc_final: 0.6918 (mt0) outliers start: 56 outliers final: 40 residues processed: 276 average time/residue: 0.3466 time to fit residues: 142.3554 Evaluate side-chains 274 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 193 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 462 ASN B 625 ASN C 94 ASN C 195 ASN C 355 ASN E 137 ASN G 39 GLN ** G 100FASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.166598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.109050 restraints weight = 22960.581| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.58 r_work: 0.2857 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 20346 Z= 0.222 Angle : 0.702 13.522 27774 Z= 0.343 Chirality : 0.047 0.230 3321 Planarity : 0.005 0.047 3402 Dihedral : 6.320 54.023 4342 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.37 % Allowed : 13.61 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2349 helix: 1.92 (0.29), residues: 372 sheet: 0.51 (0.19), residues: 753 loop : -0.67 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 112 HIS 0.010 0.001 HIS J 91 PHE 0.026 0.002 PHE A 383 TYR 0.018 0.002 TYR I 91 ARG 0.010 0.001 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 45) link_NAG-ASN : angle 2.49506 ( 135) link_BETA1-4 : bond 0.00527 ( 36) link_BETA1-4 : angle 1.38766 ( 108) link_ALPHA1-2 : bond 0.00291 ( 3) link_ALPHA1-2 : angle 1.72720 ( 9) link_ALPHA1-3 : bond 0.01141 ( 3) link_ALPHA1-3 : angle 1.80795 ( 9) hydrogen bonds : bond 0.05713 ( 704) hydrogen bonds : angle 4.72953 ( 1887) SS BOND : bond 0.00533 ( 42) SS BOND : angle 2.23983 ( 84) covalent geometry : bond 0.00556 (20217) covalent geometry : angle 0.66533 (27429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8303 (tp30) cc_final: 0.7978 (tp30) REVERT: A 190 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8304 (mm-30) REVERT: A 457 ASP cc_start: 0.7860 (t0) cc_final: 0.7644 (t0) REVERT: A 500 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8125 (mtt90) REVERT: B 621 GLU cc_start: 0.8039 (pt0) cc_final: 0.7826 (pt0) REVERT: B 653 GLN cc_start: 0.7598 (tt0) cc_final: 0.7199 (mt0) REVERT: C 303 THR cc_start: 0.8923 (m) cc_final: 0.8692 (p) REVERT: C 308 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8420 (mpt-90) REVERT: C 501 CYS cc_start: 0.8466 (p) cc_final: 0.8030 (p) REVERT: D 612 SER cc_start: 0.8572 (m) cc_final: 0.8284 (t) REVERT: D 621 GLU cc_start: 0.8029 (pt0) cc_final: 0.7592 (mm-30) REVERT: D 632 ASP cc_start: 0.8506 (t70) cc_final: 0.8255 (t0) REVERT: D 654 GLU cc_start: 0.7558 (tp30) cc_final: 0.7158 (mm-30) REVERT: E 114 GLN cc_start: 0.8587 (mt0) cc_final: 0.8105 (tt0) REVERT: E 308 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8428 (mtt-85) REVERT: F 612 SER cc_start: 0.8751 (m) cc_final: 0.8406 (t) REVERT: F 621 GLU cc_start: 0.8094 (pt0) cc_final: 0.7481 (mt-10) REVERT: F 632 ASP cc_start: 0.8441 (t70) cc_final: 0.8233 (t0) REVERT: F 653 GLN cc_start: 0.7688 (tt0) cc_final: 0.7364 (mt0) REVERT: F 654 GLU cc_start: 0.7364 (tp30) cc_final: 0.6967 (mm-30) outliers start: 70 outliers final: 51 residues processed: 306 average time/residue: 0.3344 time to fit residues: 152.6838 Evaluate side-chains 294 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN C 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.111753 restraints weight = 22925.325| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.69 r_work: 0.2910 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.003 0.057 20346 Z= 0.120 Angle : 0.553 11.488 27774 Z= 0.272 Chirality : 0.043 0.245 3321 Planarity : 0.004 0.046 3402 Dihedral : 5.692 56.622 4342 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.03 % Allowed : 14.81 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2349 helix: 2.20 (0.29), residues: 375 sheet: 0.66 (0.19), residues: 762 loop : -0.62 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 623 HIS 0.004 0.001 HIS J 91 PHE 0.017 0.001 PHE A 383 TYR 0.011 0.001 TYR K 91 ARG 0.009 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 45) link_NAG-ASN : angle 2.23347 ( 135) link_BETA1-4 : bond 0.00493 ( 36) link_BETA1-4 : angle 1.19494 ( 108) link_ALPHA1-2 : bond 0.00298 ( 3) link_ALPHA1-2 : angle 1.72014 ( 9) link_ALPHA1-3 : bond 0.01146 ( 3) link_ALPHA1-3 : angle 1.50818 ( 9) hydrogen bonds : bond 0.04042 ( 704) hydrogen bonds : angle 4.34744 ( 1887) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.46504 ( 84) covalent geometry : bond 0.00286 (20217) covalent geometry : angle 0.52027 (27429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7939 (mtt90) REVERT: B 621 GLU cc_start: 0.7799 (pt0) cc_final: 0.7595 (mm-30) REVERT: B 633 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8420 (mtpt) REVERT: B 653 GLN cc_start: 0.7477 (tt0) cc_final: 0.7100 (mt0) REVERT: D 612 SER cc_start: 0.8563 (m) cc_final: 0.8292 (t) REVERT: D 621 GLU cc_start: 0.7795 (pt0) cc_final: 0.7506 (mm-30) REVERT: D 632 ASP cc_start: 0.8344 (t70) cc_final: 0.8142 (t0) REVERT: D 654 GLU cc_start: 0.7254 (tp30) cc_final: 0.6869 (mm-30) REVERT: E 114 GLN cc_start: 0.8379 (mt0) cc_final: 0.7915 (tt0) REVERT: E 308 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8232 (mpt-90) REVERT: F 612 SER cc_start: 0.8753 (m) cc_final: 0.8399 (t) REVERT: F 621 GLU cc_start: 0.7853 (pt0) cc_final: 0.7555 (mm-30) REVERT: F 632 ASP cc_start: 0.8303 (t70) cc_final: 0.8090 (t0) REVERT: F 633 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8398 (mtpt) REVERT: F 653 GLN cc_start: 0.7638 (tt0) cc_final: 0.7300 (mt0) REVERT: F 654 GLU cc_start: 0.7071 (tp30) cc_final: 0.6797 (mm-30) REVERT: H 4 MET cc_start: 0.7282 (tpp) cc_final: 0.7030 (tpt) REVERT: J 3 GLN cc_start: 0.8164 (tt0) cc_final: 0.7238 (mp10) REVERT: L 3 GLN cc_start: 0.7366 (pm20) cc_final: 0.7020 (mp10) outliers start: 63 outliers final: 44 residues processed: 294 average time/residue: 0.3307 time to fit residues: 144.6014 Evaluate side-chains 285 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 110 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 ASN E 462 ASN K 39 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.167375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122622 restraints weight = 22900.982| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 5.62 r_work: 0.2845 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20346 Z= 0.165 Angle : 0.607 11.754 27774 Z= 0.297 Chirality : 0.044 0.247 3321 Planarity : 0.004 0.046 3402 Dihedral : 5.605 51.825 4342 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.32 % Allowed : 15.15 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2349 helix: 1.71 (0.29), residues: 393 sheet: 0.61 (0.19), residues: 768 loop : -0.54 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.007 0.001 HIS J 91 PHE 0.021 0.002 PHE A 383 TYR 0.013 0.001 TYR I 91 ARG 0.010 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 45) link_NAG-ASN : angle 2.27955 ( 135) link_BETA1-4 : bond 0.00496 ( 36) link_BETA1-4 : angle 1.22553 ( 108) link_ALPHA1-2 : bond 0.00302 ( 3) link_ALPHA1-2 : angle 1.67422 ( 9) link_ALPHA1-3 : bond 0.01109 ( 3) link_ALPHA1-3 : angle 1.44667 ( 9) hydrogen bonds : bond 0.04619 ( 704) hydrogen bonds : angle 4.46380 ( 1887) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.65617 ( 84) covalent geometry : bond 0.00410 (20217) covalent geometry : angle 0.57576 (27429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7359 (tpp) cc_final: 0.7072 (ttt) REVERT: A 457 ASP cc_start: 0.7698 (t0) cc_final: 0.7440 (t0) REVERT: A 500 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8035 (mtt90) REVERT: B 621 GLU cc_start: 0.7835 (pt0) cc_final: 0.7628 (mm-30) REVERT: B 633 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8450 (mtpt) REVERT: B 653 GLN cc_start: 0.7575 (tt0) cc_final: 0.7195 (mt0) REVERT: C 303 THR cc_start: 0.8901 (m) cc_final: 0.8686 (p) REVERT: C 360 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7934 (mtp85) REVERT: D 612 SER cc_start: 0.8590 (m) cc_final: 0.8334 (t) REVERT: D 621 GLU cc_start: 0.7917 (pt0) cc_final: 0.7572 (mm-30) REVERT: D 632 ASP cc_start: 0.8418 (t70) cc_final: 0.8212 (t0) REVERT: D 654 GLU cc_start: 0.7450 (tp30) cc_final: 0.7094 (mm-30) REVERT: E 114 GLN cc_start: 0.8459 (mt0) cc_final: 0.8007 (tt0) REVERT: E 308 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8366 (mpt-90) REVERT: F 612 SER cc_start: 0.8732 (m) cc_final: 0.8378 (t) REVERT: F 621 GLU cc_start: 0.7959 (pt0) cc_final: 0.7578 (mm-30) REVERT: F 632 ASP cc_start: 0.8369 (t70) cc_final: 0.8156 (t0) REVERT: F 633 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8453 (mtpt) REVERT: F 653 GLN cc_start: 0.7581 (tt0) cc_final: 0.7252 (mt0) REVERT: F 654 GLU cc_start: 0.7127 (tp30) cc_final: 0.6838 (mm-30) REVERT: H 4 MET cc_start: 0.7329 (tpp) cc_final: 0.7042 (tpt) REVERT: J 3 GLN cc_start: 0.8164 (tt0) cc_final: 0.7158 (mp10) outliers start: 69 outliers final: 56 residues processed: 301 average time/residue: 0.3610 time to fit residues: 162.1955 Evaluate side-chains 302 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116220 restraints weight = 22576.131| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.82 r_work: 0.2890 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20346 Z= 0.121 Angle : 0.564 11.261 27774 Z= 0.277 Chirality : 0.043 0.250 3321 Planarity : 0.004 0.045 3402 Dihedral : 5.301 48.986 4342 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.79 % Allowed : 15.97 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2349 helix: 1.86 (0.29), residues: 393 sheet: 0.65 (0.19), residues: 768 loop : -0.51 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.005 0.001 HIS L 91 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR E 173 ARG 0.010 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 45) link_NAG-ASN : angle 2.21055 ( 135) link_BETA1-4 : bond 0.00485 ( 36) link_BETA1-4 : angle 1.16511 ( 108) link_ALPHA1-2 : bond 0.00301 ( 3) link_ALPHA1-2 : angle 1.67446 ( 9) link_ALPHA1-3 : bond 0.01066 ( 3) link_ALPHA1-3 : angle 1.35401 ( 9) hydrogen bonds : bond 0.03970 ( 704) hydrogen bonds : angle 4.33779 ( 1887) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.55014 ( 84) covalent geometry : bond 0.00291 (20217) covalent geometry : angle 0.53271 (27429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7658 (t0) cc_final: 0.7365 (t0) REVERT: A 500 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7963 (mtt90) REVERT: B 621 GLU cc_start: 0.7774 (pt0) cc_final: 0.7562 (mm-30) REVERT: B 633 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8429 (mtpt) REVERT: B 653 GLN cc_start: 0.7548 (tt0) cc_final: 0.7188 (mt0) REVERT: D 612 SER cc_start: 0.8586 (m) cc_final: 0.8306 (t) REVERT: D 621 GLU cc_start: 0.7832 (pt0) cc_final: 0.7515 (mm-30) REVERT: D 632 ASP cc_start: 0.8295 (t70) cc_final: 0.8081 (t0) REVERT: D 654 GLU cc_start: 0.7326 (tp30) cc_final: 0.7001 (mm-30) REVERT: E 114 GLN cc_start: 0.8398 (mt0) cc_final: 0.7942 (tt0) REVERT: E 308 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8241 (mpt-90) REVERT: F 612 SER cc_start: 0.8711 (m) cc_final: 0.8367 (t) REVERT: F 621 GLU cc_start: 0.7900 (pt0) cc_final: 0.7493 (mm-30) REVERT: F 632 ASP cc_start: 0.8344 (t70) cc_final: 0.8117 (t0) REVERT: F 633 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8473 (mtpt) REVERT: F 654 GLU cc_start: 0.7080 (tp30) cc_final: 0.6686 (mm-30) REVERT: H 4 MET cc_start: 0.7329 (tpp) cc_final: 0.7009 (tpt) REVERT: J 3 GLN cc_start: 0.8100 (tt0) cc_final: 0.7156 (mp10) outliers start: 58 outliers final: 51 residues processed: 286 average time/residue: 0.3381 time to fit residues: 144.3585 Evaluate side-chains 296 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 355 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.171872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117544 restraints weight = 22962.432| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.90 r_work: 0.3007 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20346 Z= 0.134 Angle : 0.573 12.002 27774 Z= 0.282 Chirality : 0.043 0.253 3321 Planarity : 0.004 0.049 3402 Dihedral : 5.124 42.609 4342 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.08 % Allowed : 16.07 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2349 helix: 1.83 (0.29), residues: 393 sheet: 0.66 (0.19), residues: 768 loop : -0.51 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.005 0.001 HIS H 91 PHE 0.019 0.001 PHE A 383 TYR 0.011 0.001 TYR I 91 ARG 0.011 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 45) link_NAG-ASN : angle 2.20384 ( 135) link_BETA1-4 : bond 0.00482 ( 36) link_BETA1-4 : angle 1.16297 ( 108) link_ALPHA1-2 : bond 0.00305 ( 3) link_ALPHA1-2 : angle 1.64287 ( 9) link_ALPHA1-3 : bond 0.00976 ( 3) link_ALPHA1-3 : angle 1.23811 ( 9) hydrogen bonds : bond 0.04134 ( 704) hydrogen bonds : angle 4.34331 ( 1887) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.60195 ( 84) covalent geometry : bond 0.00328 (20217) covalent geometry : angle 0.54203 (27429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7398 (mt) cc_final: 0.7116 (mm) REVERT: A 500 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8094 (mtt90) REVERT: B 621 GLU cc_start: 0.7921 (pt0) cc_final: 0.7605 (mm-30) REVERT: B 653 GLN cc_start: 0.7568 (tt0) cc_final: 0.7190 (mt0) REVERT: D 612 SER cc_start: 0.8558 (m) cc_final: 0.8304 (t) REVERT: D 621 GLU cc_start: 0.8001 (pt0) cc_final: 0.7536 (mm-30) REVERT: D 632 ASP cc_start: 0.8398 (t70) cc_final: 0.8152 (t0) REVERT: D 654 GLU cc_start: 0.7524 (tp30) cc_final: 0.7224 (mm-30) REVERT: E 114 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: E 308 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8490 (mpt-90) REVERT: F 612 SER cc_start: 0.8649 (m) cc_final: 0.8323 (t) REVERT: F 621 GLU cc_start: 0.8090 (pt0) cc_final: 0.7596 (mm-30) REVERT: F 632 ASP cc_start: 0.8440 (t70) cc_final: 0.8211 (t0) REVERT: F 633 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8489 (mtpt) REVERT: F 654 GLU cc_start: 0.7226 (tp30) cc_final: 0.6925 (mm-30) REVERT: H 4 MET cc_start: 0.7389 (tpp) cc_final: 0.7022 (tpt) REVERT: J 3 GLN cc_start: 0.8079 (tt0) cc_final: 0.7059 (mp10) REVERT: K 82 MET cc_start: 0.3622 (OUTLIER) cc_final: 0.3202 (mpp) outliers start: 64 outliers final: 55 residues processed: 291 average time/residue: 0.3490 time to fit residues: 151.2899 Evaluate side-chains 298 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 102 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 355 ASN C 462 ASN ** F 540 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 = 0.3842 r_free = 0.3842 target = 0.170904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.113186 restraints weight = 22602.121| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.87 r_work: 0.2924 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20346 Z= 0.171 Angle : 0.624 12.381 27774 Z= 0.305 Chirality : 0.045 0.255 3321 Planarity : 0.004 0.053 3402 Dihedral : 5.231 42.654 4342 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.98 % Allowed : 16.59 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2349 helix: 1.68 (0.29), residues: 390 sheet: 0.64 (0.19), residues: 750 loop : -0.52 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.007 0.001 HIS H 91 PHE 0.022 0.002 PHE A 383 TYR 0.013 0.001 TYR K 91 ARG 0.013 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 45) link_NAG-ASN : angle 2.35570 ( 135) link_BETA1-4 : bond 0.00489 ( 36) link_BETA1-4 : angle 1.20437 ( 108) link_ALPHA1-2 : bond 0.00272 ( 3) link_ALPHA1-2 : angle 1.66782 ( 9) link_ALPHA1-3 : bond 0.00916 ( 3) link_ALPHA1-3 : angle 1.11382 ( 9) hydrogen bonds : bond 0.04749 ( 704) hydrogen bonds : angle 4.47357 ( 1887) SS BOND : bond 0.00434 ( 42) SS BOND : angle 1.88824 ( 84) covalent geometry : bond 0.00423 (20217) covalent geometry : angle 0.59043 (27429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8084 (tp30) cc_final: 0.7781 (tp30) REVERT: A 308 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8323 (mtp-110) REVERT: A 358 ILE cc_start: 0.7443 (mt) cc_final: 0.7181 (mm) REVERT: A 457 ASP cc_start: 0.7659 (t0) cc_final: 0.7367 (t0) REVERT: A 500 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8034 (mtt90) REVERT: B 653 GLN cc_start: 0.7691 (tt0) cc_final: 0.7287 (mt0) REVERT: C 66 HIS cc_start: 0.6390 (m90) cc_final: 0.6160 (m-70) REVERT: D 612 SER cc_start: 0.8570 (m) cc_final: 0.8332 (t) REVERT: D 621 GLU cc_start: 0.7852 (pt0) cc_final: 0.7499 (mm-30) REVERT: D 632 ASP cc_start: 0.8325 (t70) cc_final: 0.8088 (t0) REVERT: D 654 GLU cc_start: 0.7597 (tp30) cc_final: 0.7314 (mm-30) REVERT: E 114 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: E 207 LYS cc_start: 0.7603 (mmtm) cc_final: 0.7030 (mtmm) REVERT: E 308 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8289 (mpt-90) REVERT: F 612 SER cc_start: 0.8746 (m) cc_final: 0.8450 (t) REVERT: F 633 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8408 (mtpt) REVERT: F 654 GLU cc_start: 0.7297 (tp30) cc_final: 0.6980 (mm-30) REVERT: J 3 GLN cc_start: 0.8055 (tt0) cc_final: 0.7086 (mp10) REVERT: K 82 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.3258 (mpp) outliers start: 62 outliers final: 52 residues processed: 294 average time/residue: 0.3481 time to fit residues: 150.9761 Evaluate side-chains 302 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 64 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 355 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.171863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114533 restraints weight = 22623.536| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.74 r_work: 0.2858 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20346 Z= 0.169 Angle : 0.618 12.445 27774 Z= 0.303 Chirality : 0.044 0.259 3321 Planarity : 0.004 0.049 3402 Dihedral : 5.223 43.723 4342 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.03 % Allowed : 16.55 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2349 helix: 1.64 (0.29), residues: 390 sheet: 0.74 (0.20), residues: 714 loop : -0.64 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 427 HIS 0.007 0.001 HIS H 91 PHE 0.021 0.002 PHE A 383 TYR 0.013 0.001 TYR K 91 ARG 0.012 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 45) link_NAG-ASN : angle 2.33756 ( 135) link_BETA1-4 : bond 0.00485 ( 36) link_BETA1-4 : angle 1.22065 ( 108) link_ALPHA1-2 : bond 0.00250 ( 3) link_ALPHA1-2 : angle 1.68370 ( 9) link_ALPHA1-3 : bond 0.00851 ( 3) link_ALPHA1-3 : angle 1.07943 ( 9) hydrogen bonds : bond 0.04665 ( 704) hydrogen bonds : angle 4.45625 ( 1887) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.84830 ( 84) covalent geometry : bond 0.00420 (20217) covalent geometry : angle 0.58501 (27429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8296 (mtp-110) REVERT: A 500 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8032 (mtt90) REVERT: B 617 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8094 (ptp-110) REVERT: B 653 GLN cc_start: 0.7646 (tt0) cc_final: 0.7202 (mt0) REVERT: C 66 HIS cc_start: 0.6404 (m90) cc_final: 0.6162 (m-70) REVERT: C 308 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8130 (mpt-90) REVERT: D 612 SER cc_start: 0.8517 (m) cc_final: 0.8296 (t) REVERT: D 621 GLU cc_start: 0.7845 (pt0) cc_final: 0.7502 (mm-30) REVERT: D 632 ASP cc_start: 0.8291 (t70) cc_final: 0.8065 (t0) REVERT: D 654 GLU cc_start: 0.7599 (tp30) cc_final: 0.7347 (mm-30) REVERT: E 114 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: E 207 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7029 (mtmm) REVERT: E 308 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8321 (mpt-90) REVERT: F 633 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8476 (mtpt) REVERT: F 654 GLU cc_start: 0.7308 (tp30) cc_final: 0.6993 (mm-30) REVERT: J 3 GLN cc_start: 0.8026 (tt0) cc_final: 0.7120 (mp10) REVERT: K 82 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.3084 (mpp) outliers start: 63 outliers final: 51 residues processed: 294 average time/residue: 0.3599 time to fit residues: 156.9144 Evaluate side-chains 303 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 164 optimal weight: 0.0000 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 637 ASN C 355 ASN D 607 ASN D 653 GLN ** F 540 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 = 0.3880 r_free = 0.3880 target = 0.174890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121475 restraints weight = 22890.733| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.92 r_work: 0.3005 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20346 Z= 0.092 Angle : 0.528 11.086 27774 Z= 0.262 Chirality : 0.041 0.261 3321 Planarity : 0.003 0.044 3402 Dihedral : 4.772 40.082 4342 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.92 % Allowed : 17.60 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2349 helix: 2.53 (0.30), residues: 357 sheet: 0.90 (0.20), residues: 714 loop : -0.60 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.002 0.001 HIS C 374 PHE 0.013 0.001 PHE A 383 TYR 0.008 0.001 TYR F 638 ARG 0.010 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 45) link_NAG-ASN : angle 2.11712 ( 135) link_BETA1-4 : bond 0.00466 ( 36) link_BETA1-4 : angle 1.11819 ( 108) link_ALPHA1-2 : bond 0.00292 ( 3) link_ALPHA1-2 : angle 1.62546 ( 9) link_ALPHA1-3 : bond 0.00711 ( 3) link_ALPHA1-3 : angle 1.20585 ( 9) hydrogen bonds : bond 0.03325 ( 704) hydrogen bonds : angle 4.14754 ( 1887) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.29787 ( 84) covalent geometry : bond 0.00207 (20217) covalent geometry : angle 0.49860 (27429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11040.90 seconds wall clock time: 191 minutes 58.63 seconds (11518.63 seconds total)