Starting phenix.real_space_refine on Tue May 20 13:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.map" model { file = "/net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euu_28617/05_2025/8euu_28617.cif" } resolution = 2.7 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= 0.036 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 129 5.16 5 C 12468 2.51 5 N 3339 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 19926 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: 13.10, per 1000 atoms: 0.66 Number of scatterers: 19926 At special positions: 0 Unit cell: (144.42, 151.89, 121.18, 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 129 16.00 O 3990 8.00 N 3339 7.00 C 12468 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=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS 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=2.03 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=2.04 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=2.04 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=2.03 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=2.03 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: 5.46 Conformation dependent library (CDL) restraints added in 2.3 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 45 sheets defined 20.3% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.992A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.814A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.065A 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 474 through 484 removed outlier: 4.258A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.164A 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 543 removed outlier: 3.615A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.620A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.773A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.959A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.696A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.081A 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 474 through 484 removed outlier: 4.251A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.115A 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: 3.647A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.552A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (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: 3.782A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.974A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.546A 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 354 removed outlier: 3.658A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.061A 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 484 removed outlier: 3.913A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.716A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.784A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.293A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 97 through 100A removed outlier: 3.501A pdb=" N ASN G 100 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.901A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.157A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 97 through 100A Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.018A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.256A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 97 through 100A Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.877A 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: 5.530A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.635A 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: 4.018A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 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 201 through 203 removed outlier: 6.416A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.489A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.466A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.626A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.669A 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: 3.808A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 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 201 through 203 removed outlier: 6.455A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.502A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.451A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.657A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.740A 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: 3.992A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.910A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) 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 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.507A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.472A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.611A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.855A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 12.065A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.272A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.883A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.861A pdb=" N THR H 97 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.650A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.797A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.596A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.880A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.860A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.201A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.816A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.071A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.913A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.870A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2025 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: 7.69 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6290 1.35 - 1.47: 5225 1.47 - 1.60: 8633 1.60 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 20322 Sorted by residual: bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.67e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.56e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.53e+00 bond pdb=" N ALA B 512 " pdb=" CA ALA B 512 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 ... (remaining 20317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26754 1.79 - 3.57: 681 3.57 - 5.36: 136 5.36 - 7.14: 16 7.14 - 8.93: 1 Bond angle restraints: 27588 Sorted by residual: angle pdb=" CB MET F 535 " pdb=" CG MET F 535 " pdb=" SD MET F 535 " ideal model delta sigma weight residual 112.70 121.63 -8.93 3.00e+00 1.11e-01 8.86e+00 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG2 ILE B 635 " ideal model delta sigma weight residual 110.50 114.72 -4.22 1.70e+00 3.46e-01 6.16e+00 angle pdb=" CA GLN A 114 " pdb=" CB GLN A 114 " pdb=" CG GLN A 114 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA ILE F 635 " pdb=" CB ILE F 635 " pdb=" CG2 ILE F 635 " ideal model delta sigma weight residual 110.50 114.54 -4.04 1.70e+00 3.46e-01 5.66e+00 angle pdb=" CA ILE D 635 " pdb=" CB ILE D 635 " pdb=" CG2 ILE D 635 " ideal model delta sigma weight residual 110.50 114.44 -3.94 1.70e+00 3.46e-01 5.38e+00 ... (remaining 27583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 11930 21.51 - 43.02: 985 43.02 - 64.52: 272 64.52 - 86.03: 57 86.03 - 107.54: 28 Dihedral angle restraints: 13272 sinusoidal: 6387 harmonic: 6885 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -152.23 66.23 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.31 62.31 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -147.00 61.00 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2796 0.055 - 0.111: 405 0.111 - 0.166: 141 0.166 - 0.222: 3 0.222 - 0.277: 9 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3351 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 24 " -0.138 9.50e-02 1.11e+02 6.22e-02 2.69e+00 pdb=" NE ARG J 24 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG J 24 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 24 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 635 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE D 635 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE D 635 " 0.010 2.00e-02 2.50e+03 pdb=" N SER D 636 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " 0.127 9.50e-02 1.11e+02 5.73e-02 2.15e+00 pdb=" NE ARG A 444 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " 0.002 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 161 2.59 - 3.17: 15684 3.17 - 3.74: 29963 3.74 - 4.32: 44876 4.32 - 4.90: 73331 Nonbonded interactions: 164015 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.012 3.040 nonbonded pdb=" O7 NAG Z 2 " pdb=" O6 NAG f 1 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.203 3.040 ... (remaining 164010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 5.220 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: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.350 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.005 0.039 20451 Z= 0.213 Angle : 0.693 8.930 27933 Z= 0.320 Chirality : 0.049 0.277 3354 Planarity : 0.003 0.062 3402 Dihedral : 17.088 107.540 8712 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.48 % Allowed : 15.83 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2352 helix: 1.87 (0.29), residues: 393 sheet: 0.93 (0.18), residues: 819 loop : 0.43 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.002 0.001 HIS E 105 PHE 0.023 0.001 PHE C 53 TYR 0.014 0.001 TYR J 36 ARG 0.010 0.001 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 45) link_NAG-ASN : angle 2.08203 ( 135) link_BETA1-4 : bond 0.00466 ( 36) link_BETA1-4 : angle 1.12532 ( 108) link_ALPHA1-2 : bond 0.00356 ( 3) link_ALPHA1-2 : angle 1.73246 ( 9) link_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 1.67511 ( 9) hydrogen bonds : bond 0.12000 ( 732) hydrogen bonds : angle 5.73306 ( 2025) SS BOND : bond 0.00264 ( 42) SS BOND : angle 1.05337 ( 84) covalent geometry : bond 0.00451 (20322) covalent geometry : angle 0.67483 (27588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 2.218 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.9058 (mmp) cc_final: 0.8585 (mmp) REVERT: D 635 ILE cc_start: 0.7335 (mp) cc_final: 0.7128 (mm) REVERT: E 95 MET cc_start: 0.8576 (ptm) cc_final: 0.8314 (ptm) REVERT: F 530 MET cc_start: 0.8384 (mtp) cc_final: 0.7904 (mtp) REVERT: F 655 LYS cc_start: 0.6671 (mtpt) cc_final: 0.5742 (pttm) REVERT: I 34 LEU cc_start: 0.8530 (tp) cc_final: 0.8161 (mt) REVERT: K 34 LEU cc_start: 0.8484 (tp) cc_final: 0.8144 (mt) REVERT: K 77 THR cc_start: 0.6727 (p) cc_final: 0.6504 (p) outliers start: 10 outliers final: 9 residues processed: 262 average time/residue: 1.2527 time to fit residues: 373.8033 Evaluate side-chains 233 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 440 GLN E 137 ASN G 32 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 105 GLN ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN L 6 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.196463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139509 restraints weight = 20855.755| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.37 r_work: 0.3356 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20451 Z= 0.206 Angle : 0.676 9.200 27933 Z= 0.332 Chirality : 0.047 0.262 3354 Planarity : 0.004 0.036 3402 Dihedral : 9.739 68.514 4366 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.02 % Allowed : 14.53 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2352 helix: 1.36 (0.28), residues: 414 sheet: 0.96 (0.18), residues: 777 loop : 0.54 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 427 HIS 0.007 0.002 HIS G 35 PHE 0.015 0.002 PHE E 383 TYR 0.023 0.002 TYR H 49 ARG 0.005 0.001 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 45) link_NAG-ASN : angle 2.96899 ( 135) link_BETA1-4 : bond 0.00614 ( 36) link_BETA1-4 : angle 1.55824 ( 108) link_ALPHA1-2 : bond 0.00398 ( 3) link_ALPHA1-2 : angle 1.96313 ( 9) link_ALPHA1-3 : bond 0.00778 ( 3) link_ALPHA1-3 : angle 1.96519 ( 9) hydrogen bonds : bond 0.04403 ( 732) hydrogen bonds : angle 5.08422 ( 2025) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.20073 ( 84) covalent geometry : bond 0.00479 (20322) covalent geometry : angle 0.63468 (27588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: A 327 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: A 444 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7332 (tpt90) REVERT: B 530 MET cc_start: 0.8332 (mtp) cc_final: 0.7979 (mtp) REVERT: C 46 LYS cc_start: 0.7887 (tttp) cc_final: 0.7567 (mmtp) REVERT: C 67 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8386 (t0) REVERT: C 151 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7434 (mtt-85) REVERT: C 189 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7876 (tttm) REVERT: C 444 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7556 (tmm-80) REVERT: E 95 MET cc_start: 0.8952 (ptm) cc_final: 0.8662 (ptm) REVERT: E 327 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7880 (ptt-90) REVERT: F 530 MET cc_start: 0.8423 (mtp) cc_final: 0.8123 (mtp) REVERT: F 617 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5540 (ttm170) REVERT: I 34 LEU cc_start: 0.7825 (tp) cc_final: 0.7533 (mt) REVERT: K 62 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5729 (pptt) REVERT: K 69 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6838 (mtm) REVERT: K 77 THR cc_start: 0.6942 (p) cc_final: 0.6705 (p) REVERT: L 46 LEU cc_start: 0.6821 (tt) cc_final: 0.6466 (tt) outliers start: 63 outliers final: 16 residues processed: 258 average time/residue: 1.3401 time to fit residues: 387.9007 Evaluate side-chains 234 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 103 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 105 GLN ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140962 restraints weight = 20900.914| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.21 r_work: 0.3384 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20451 Z= 0.135 Angle : 0.576 8.447 27933 Z= 0.283 Chirality : 0.043 0.246 3354 Planarity : 0.003 0.036 3402 Dihedral : 8.053 59.421 4356 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.49 % Allowed : 15.83 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2352 helix: 1.47 (0.28), residues: 414 sheet: 0.98 (0.18), residues: 777 loop : 0.51 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 427 HIS 0.003 0.001 HIS I 35 PHE 0.014 0.001 PHE E 383 TYR 0.019 0.002 TYR H 49 ARG 0.004 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 45) link_NAG-ASN : angle 2.71631 ( 135) link_BETA1-4 : bond 0.00476 ( 36) link_BETA1-4 : angle 1.44001 ( 108) link_ALPHA1-2 : bond 0.00137 ( 3) link_ALPHA1-2 : angle 1.63965 ( 9) link_ALPHA1-3 : bond 0.01012 ( 3) link_ALPHA1-3 : angle 1.33245 ( 9) hydrogen bonds : bond 0.03822 ( 732) hydrogen bonds : angle 4.83323 ( 2025) SS BOND : bond 0.00311 ( 42) SS BOND : angle 0.86760 ( 84) covalent geometry : bond 0.00306 (20322) covalent geometry : angle 0.53641 (27588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 2.031 Fit side-chains REVERT: A 103 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: C 46 LYS cc_start: 0.7909 (tttp) cc_final: 0.7608 (mmtp) REVERT: C 151 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7463 (mtt-85) REVERT: C 189 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (tttm) REVERT: C 327 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7839 (ptt-90) REVERT: C 444 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7472 (tmm-80) REVERT: C 502 LYS cc_start: 0.8207 (tttp) cc_final: 0.7871 (tttp) REVERT: D 658 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: E 327 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: F 530 MET cc_start: 0.8379 (mtp) cc_final: 0.7964 (mtp) REVERT: F 660 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7153 (tp) REVERT: I 34 LEU cc_start: 0.7891 (tp) cc_final: 0.7494 (mt) REVERT: K 34 LEU cc_start: 0.7855 (tp) cc_final: 0.7632 (tp) REVERT: K 62 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5866 (pptt) REVERT: K 69 MET cc_start: 0.7476 (mtm) cc_final: 0.6819 (mtm) outliers start: 52 outliers final: 19 residues processed: 260 average time/residue: 1.3839 time to fit residues: 404.8448 Evaluate side-chains 234 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 HIS I 32 ASN I 105 GLN ** L 90 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.198080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141496 restraints weight = 20925.321| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.29 r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20451 Z= 0.118 Angle : 0.554 8.484 27933 Z= 0.273 Chirality : 0.043 0.248 3354 Planarity : 0.003 0.036 3402 Dihedral : 6.727 59.439 4356 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.45 % Allowed : 16.79 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2352 helix: 1.58 (0.28), residues: 414 sheet: 0.97 (0.18), residues: 777 loop : 0.43 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 427 HIS 0.003 0.001 HIS K 35 PHE 0.013 0.001 PHE E 383 TYR 0.019 0.001 TYR A 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 45) link_NAG-ASN : angle 2.62402 ( 135) link_BETA1-4 : bond 0.00441 ( 36) link_BETA1-4 : angle 1.42266 ( 108) link_ALPHA1-2 : bond 0.00244 ( 3) link_ALPHA1-2 : angle 1.67197 ( 9) link_ALPHA1-3 : bond 0.00933 ( 3) link_ALPHA1-3 : angle 1.27211 ( 9) hydrogen bonds : bond 0.03625 ( 732) hydrogen bonds : angle 4.70687 ( 2025) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.80214 ( 84) covalent geometry : bond 0.00267 (20322) covalent geometry : angle 0.51578 (27588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: C 46 LYS cc_start: 0.7874 (tttp) cc_final: 0.7574 (mmtp) REVERT: C 67 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 97 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8132 (mppt) REVERT: C 151 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7467 (mtt-85) REVERT: C 189 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.8000 (tttt) REVERT: C 327 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7815 (ptt-90) REVERT: C 444 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7481 (tmm-80) REVERT: D 658 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: E 103 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: E 327 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (ptt-90) REVERT: F 530 MET cc_start: 0.8402 (mtp) cc_final: 0.8139 (mtp) REVERT: F 660 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7126 (tp) REVERT: I 34 LEU cc_start: 0.7872 (tp) cc_final: 0.7481 (mt) REVERT: K 69 MET cc_start: 0.7486 (mtm) cc_final: 0.6852 (mtm) REVERT: K 100 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6909 (pt0) outliers start: 51 outliers final: 22 residues processed: 257 average time/residue: 1.3201 time to fit residues: 384.0282 Evaluate side-chains 241 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 173 optimal weight: 4.9990 chunk 229 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN C 462 ASN F 543 ASN F 658 GLN I 105 GLN J 90 HIS K 32 ASN L 90 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138877 restraints weight = 20999.989| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.22 r_work: 0.3346 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 20451 Z= 0.324 Angle : 0.773 10.330 27933 Z= 0.378 Chirality : 0.051 0.275 3354 Planarity : 0.005 0.042 3402 Dihedral : 7.063 59.573 4356 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.84 % Allowed : 15.97 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.75 (0.17), residues: 2352 helix: 0.87 (0.27), residues: 396 sheet: 0.72 (0.18), residues: 768 loop : 0.36 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 427 HIS 0.006 0.002 HIS K 35 PHE 0.016 0.002 PHE E 383 TYR 0.028 0.002 TYR C 384 ARG 0.006 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 45) link_NAG-ASN : angle 3.42387 ( 135) link_BETA1-4 : bond 0.00534 ( 36) link_BETA1-4 : angle 1.79654 ( 108) link_ALPHA1-2 : bond 0.00211 ( 3) link_ALPHA1-2 : angle 1.85299 ( 9) link_ALPHA1-3 : bond 0.00718 ( 3) link_ALPHA1-3 : angle 1.17912 ( 9) hydrogen bonds : bond 0.05126 ( 732) hydrogen bonds : angle 5.16953 ( 2025) SS BOND : bond 0.00524 ( 42) SS BOND : angle 1.46788 ( 84) covalent geometry : bond 0.00772 (20322) covalent geometry : angle 0.72637 (27588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 201 time to evaluate : 1.994 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: B 584 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 46 LYS cc_start: 0.7937 (tttp) cc_final: 0.7624 (mmtp) REVERT: C 103 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: C 327 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7796 (ptt-90) REVERT: C 444 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7678 (tmm-80) REVERT: D 658 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: E 91 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: E 327 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (ptt-90) REVERT: F 530 MET cc_start: 0.8469 (mtp) cc_final: 0.8051 (mtp) REVERT: I 34 LEU cc_start: 0.7962 (tp) cc_final: 0.7660 (tp) REVERT: I 100 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6908 (pt0) REVERT: K 75 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7497 (pt) REVERT: K 100 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7087 (pt0) outliers start: 80 outliers final: 35 residues processed: 259 average time/residue: 1.4073 time to fit residues: 408.2703 Evaluate side-chains 242 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 175 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.198574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142255 restraints weight = 20873.247| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.30 r_work: 0.3397 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20451 Z= 0.136 Angle : 0.586 9.407 27933 Z= 0.288 Chirality : 0.043 0.248 3354 Planarity : 0.003 0.036 3402 Dihedral : 6.018 53.292 4356 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 17.60 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.93 (0.18), residues: 2352 helix: 1.26 (0.27), residues: 414 sheet: 0.89 (0.18), residues: 762 loop : 0.33 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 427 HIS 0.003 0.001 HIS K 35 PHE 0.014 0.001 PHE E 383 TYR 0.018 0.001 TYR A 173 ARG 0.004 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.87449 ( 135) link_BETA1-4 : bond 0.00397 ( 36) link_BETA1-4 : angle 1.50998 ( 108) link_ALPHA1-2 : bond 0.00159 ( 3) link_ALPHA1-2 : angle 1.80197 ( 9) link_ALPHA1-3 : bond 0.00843 ( 3) link_ALPHA1-3 : angle 1.09654 ( 9) hydrogen bonds : bond 0.03904 ( 732) hydrogen bonds : angle 4.81392 ( 2025) SS BOND : bond 0.00432 ( 42) SS BOND : angle 0.99150 ( 84) covalent geometry : bond 0.00311 (20322) covalent geometry : angle 0.54158 (27588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7873 (ptt-90) REVERT: B 584 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 46 LYS cc_start: 0.7926 (tttp) cc_final: 0.7651 (mmtp) REVERT: C 97 LYS cc_start: 0.8526 (mmtp) cc_final: 0.8152 (mppt) REVERT: C 327 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7879 (ptt-90) REVERT: C 444 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7558 (tmm-80) REVERT: D 635 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7153 (mm) REVERT: D 658 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: E 103 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: E 327 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7840 (ptt-90) REVERT: I 34 LEU cc_start: 0.7982 (tp) cc_final: 0.7521 (mt) REVERT: I 100 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: K 76 ASN cc_start: 0.7490 (m-40) cc_final: 0.7250 (m110) REVERT: K 100 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6952 (pt0) outliers start: 49 outliers final: 23 residues processed: 246 average time/residue: 1.3864 time to fit residues: 383.1391 Evaluate side-chains 231 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 226 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.197152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141122 restraints weight = 20762.776| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.33 r_work: 0.3378 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20451 Z= 0.202 Angle : 0.644 9.826 27933 Z= 0.316 Chirality : 0.045 0.258 3354 Planarity : 0.004 0.036 3402 Dihedral : 5.995 51.575 4356 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.45 % Allowed : 17.60 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.84 (0.18), residues: 2352 helix: 1.17 (0.27), residues: 414 sheet: 0.77 (0.18), residues: 777 loop : 0.31 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 427 HIS 0.004 0.001 HIS C 85 PHE 0.015 0.002 PHE E 383 TYR 0.019 0.002 TYR A 173 ARG 0.003 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 45) link_NAG-ASN : angle 3.00129 ( 135) link_BETA1-4 : bond 0.00431 ( 36) link_BETA1-4 : angle 1.55053 ( 108) link_ALPHA1-2 : bond 0.00220 ( 3) link_ALPHA1-2 : angle 1.82113 ( 9) link_ALPHA1-3 : bond 0.00798 ( 3) link_ALPHA1-3 : angle 1.05074 ( 9) hydrogen bonds : bond 0.04306 ( 732) hydrogen bonds : angle 4.91813 ( 2025) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.20171 ( 84) covalent geometry : bond 0.00474 (20322) covalent geometry : angle 0.60014 (27588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 2.217 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7837 (ptt-90) REVERT: B 584 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7544 (mt-10) REVERT: C 46 LYS cc_start: 0.7929 (tttp) cc_final: 0.7651 (mmtp) REVERT: C 327 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7856 (ptt-90) REVERT: C 444 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7480 (tmm-80) REVERT: D 635 ILE cc_start: 0.7374 (mp) cc_final: 0.7139 (mm) REVERT: D 658 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: E 103 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: E 327 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7736 (ptt-90) REVERT: G 75 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7202 (pt) REVERT: I 34 LEU cc_start: 0.8022 (tp) cc_final: 0.7601 (tp) REVERT: I 100 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: J 32 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: K 76 ASN cc_start: 0.7540 (m-40) cc_final: 0.7329 (m110) REVERT: K 100 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6985 (pt0) outliers start: 51 outliers final: 26 residues processed: 243 average time/residue: 1.3956 time to fit residues: 380.4495 Evaluate side-chains 236 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 226 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN B 543 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 ASN F 607 ASN F 658 GLN I 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.193875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139390 restraints weight = 20973.855| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3329 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 20451 Z= 0.339 Angle : 0.797 10.460 27933 Z= 0.390 Chirality : 0.052 0.273 3354 Planarity : 0.005 0.050 3402 Dihedral : 6.710 56.599 4356 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.26 % Allowed : 17.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.43 (0.17), residues: 2352 helix: 0.43 (0.26), residues: 414 sheet: 0.56 (0.18), residues: 771 loop : 0.18 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 427 HIS 0.007 0.002 HIS C 85 PHE 0.017 0.003 PHE E 383 TYR 0.030 0.003 TYR C 384 ARG 0.004 0.001 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 45) link_NAG-ASN : angle 3.50663 ( 135) link_BETA1-4 : bond 0.00520 ( 36) link_BETA1-4 : angle 1.82139 ( 108) link_ALPHA1-2 : bond 0.00122 ( 3) link_ALPHA1-2 : angle 2.00402 ( 9) link_ALPHA1-3 : bond 0.00686 ( 3) link_ALPHA1-3 : angle 1.16468 ( 9) hydrogen bonds : bond 0.05261 ( 732) hydrogen bonds : angle 5.23165 ( 2025) SS BOND : bond 0.00611 ( 42) SS BOND : angle 1.62732 ( 84) covalent geometry : bond 0.00811 (20322) covalent geometry : angle 0.74886 (27588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 198 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7752 (ptt-90) REVERT: B 584 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7297 (mt-10) REVERT: C 46 LYS cc_start: 0.7886 (tttp) cc_final: 0.7507 (mmtp) REVERT: C 327 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7704 (ptt-90) REVERT: C 444 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7587 (tmm-80) REVERT: D 584 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7347 (mt-10) REVERT: D 658 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: E 327 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7628 (ptt-90) REVERT: E 455 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8382 (t) REVERT: G 75 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7277 (pt) REVERT: I 34 LEU cc_start: 0.7918 (tp) cc_final: 0.7467 (tp) REVERT: I 100 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: K 75 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7463 (pt) REVERT: K 100 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6955 (pt0) outliers start: 68 outliers final: 36 residues processed: 248 average time/residue: 1.3802 time to fit residues: 383.7603 Evaluate side-chains 239 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 117 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141075 restraints weight = 20845.434| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.22 r_work: 0.3384 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20451 Z= 0.135 Angle : 0.601 9.538 27933 Z= 0.296 Chirality : 0.043 0.243 3354 Planarity : 0.004 0.035 3402 Dihedral : 5.859 59.765 4356 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.21 % Allowed : 18.56 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.81 (0.18), residues: 2352 helix: 1.10 (0.27), residues: 414 sheet: 0.78 (0.18), residues: 744 loop : 0.29 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 427 HIS 0.004 0.001 HIS K 35 PHE 0.013 0.001 PHE A 383 TYR 0.021 0.001 TYR A 173 ARG 0.004 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 45) link_NAG-ASN : angle 2.91612 ( 135) link_BETA1-4 : bond 0.00368 ( 36) link_BETA1-4 : angle 1.53897 ( 108) link_ALPHA1-2 : bond 0.00144 ( 3) link_ALPHA1-2 : angle 1.83745 ( 9) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 1.05803 ( 9) hydrogen bonds : bond 0.04001 ( 732) hydrogen bonds : angle 4.85425 ( 2025) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.03549 ( 84) covalent geometry : bond 0.00306 (20322) covalent geometry : angle 0.55668 (27588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: A 327 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: B 584 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 46 LYS cc_start: 0.7948 (tttp) cc_final: 0.7676 (mmtp) REVERT: C 327 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7873 (ptt-90) REVERT: C 444 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7475 (tmm-80) REVERT: D 635 ILE cc_start: 0.7366 (mp) cc_final: 0.7126 (mm) REVERT: D 658 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: E 103 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: G 75 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7316 (pt) REVERT: K 76 ASN cc_start: 0.7760 (m-40) cc_final: 0.7558 (m110) REVERT: K 100 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6946 (pt0) outliers start: 46 outliers final: 25 residues processed: 243 average time/residue: 1.4456 time to fit residues: 394.4881 Evaluate side-chains 233 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 197 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN I 105 GLN K 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141322 restraints weight = 20888.833| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.01 r_work: 0.3365 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20451 Z= 0.201 Angle : 0.650 9.830 27933 Z= 0.319 Chirality : 0.045 0.253 3354 Planarity : 0.004 0.035 3402 Dihedral : 5.893 59.651 4356 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 19.09 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.73 (0.18), residues: 2352 helix: 1.06 (0.27), residues: 414 sheet: 0.65 (0.18), residues: 780 loop : 0.29 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 427 HIS 0.004 0.001 HIS C 85 PHE 0.015 0.002 PHE E 383 TYR 0.023 0.002 TYR A 173 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 45) link_NAG-ASN : angle 3.02449 ( 135) link_BETA1-4 : bond 0.00421 ( 36) link_BETA1-4 : angle 1.56446 ( 108) link_ALPHA1-2 : bond 0.00165 ( 3) link_ALPHA1-2 : angle 1.85183 ( 9) link_ALPHA1-3 : bond 0.00802 ( 3) link_ALPHA1-3 : angle 1.03208 ( 9) hydrogen bonds : bond 0.04335 ( 732) hydrogen bonds : angle 4.92129 ( 2025) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.20266 ( 84) covalent geometry : bond 0.00472 (20322) covalent geometry : angle 0.60593 (27588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: A 327 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (ptt-90) REVERT: B 584 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 46 LYS cc_start: 0.7871 (tttp) cc_final: 0.7561 (mmtp) REVERT: C 327 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7822 (ptt-90) REVERT: C 444 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7442 (tmm-80) REVERT: D 635 ILE cc_start: 0.7312 (mp) cc_final: 0.7064 (mm) REVERT: D 658 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: E 103 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: G 75 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7298 (pt) REVERT: K 100 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6819 (pt0) outliers start: 40 outliers final: 27 residues processed: 232 average time/residue: 1.4354 time to fit residues: 372.2132 Evaluate side-chains 234 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN K 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.197197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141329 restraints weight = 21033.661| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.45 r_work: 0.3361 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20451 Z= 0.154 Angle : 0.611 9.740 27933 Z= 0.301 Chirality : 0.044 0.245 3354 Planarity : 0.004 0.036 3402 Dihedral : 5.708 59.976 4356 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.11 % Allowed : 18.90 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.81 (0.18), residues: 2352 helix: 1.17 (0.27), residues: 414 sheet: 0.73 (0.18), residues: 768 loop : 0.30 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 427 HIS 0.004 0.001 HIS I 35 PHE 0.013 0.001 PHE E 383 TYR 0.024 0.002 TYR A 173 ARG 0.004 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 45) link_NAG-ASN : angle 2.92373 ( 135) link_BETA1-4 : bond 0.00393 ( 36) link_BETA1-4 : angle 1.51871 ( 108) link_ALPHA1-2 : bond 0.00185 ( 3) link_ALPHA1-2 : angle 1.81634 ( 9) link_ALPHA1-3 : bond 0.00822 ( 3) link_ALPHA1-3 : angle 1.01881 ( 9) hydrogen bonds : bond 0.04069 ( 732) hydrogen bonds : angle 4.83741 ( 2025) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.07682 ( 84) covalent geometry : bond 0.00356 (20322) covalent geometry : angle 0.56766 (27588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17068.59 seconds wall clock time: 293 minutes 52.59 seconds (17632.59 seconds total)