Starting phenix.real_space_refine on Fri Feb 6 12:24:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q0w_72108/02_2026/9q0w_72108.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 138 5.16 5 C 15465 2.51 5 N 4134 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24735 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: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1615 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "I" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Chain: "J" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1615 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "K" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 219} Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1615 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.74, per 1000 atoms: 0.27 Number of scatterers: 24735 At special positions: 0 Unit cell: (154.38, 158.53, 186.75, 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 138 16.00 O 4998 8.00 N 4134 7.00 C 15465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 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 G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 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 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 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 355 " " NAG A 606 " - " 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 355 " " NAG C 606 " - " 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 355 " " NAG E 606 " - " 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 53 sheets defined 17.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.074A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.932A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.696A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.749A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.924A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.913A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.824A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.036A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.578A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.578A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.985A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.705A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.615A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.940A 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: 4.067A 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: 3.880A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.027A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.628A pdb=" N THR G 131 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER G 132 " --> pdb=" O ARG G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.548A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 127 through 132 removed outlier: 3.624A pdb=" N THR I 131 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER I 132 " --> pdb=" O ARG I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.589A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 127 Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.692A pdb=" N GLU K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 127 through 132 removed outlier: 3.624A pdb=" N THR K 131 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER K 132 " --> pdb=" O ARG K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.949A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.210A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.231A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.350A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 7.192A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.408A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 519 removed outlier: 6.201A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA G 100A" --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY G 100H" --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE G 100 " --> pdb=" O SER G 100F" (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER G 100F" --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.581A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.582A 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 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 removed outlier: 3.748A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) 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 Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.239A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.171A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 516 through 519 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 516 through 519 current: chain 'I' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100E through 100I Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.371A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.769A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.605A 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: 6.706A 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 Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 261 current: chain 'E' and resid 284 through 298 removed outlier: 7.117A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC8, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.753A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 517 through 519 removed outlier: 6.119A pdb=" N VAL F 518 " --> pdb=" O TYR K 99 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA K 100A" --> pdb=" O VAL F 518 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS K 97 " --> pdb=" O GLY K 100H" (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY K 100H" --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR K 99 " --> pdb=" O SER K 100F" (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER K 100F" --> pdb=" O TYR K 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 100A" --> pdb=" O TYR K 100D" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 11 through 13 current: chain 'G' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'G' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 145 current: chain 'G' and resid 176 through 185 Processing sheet with id=AD4, first strand: chain 'G' and resid 151 through 154 removed outlier: 4.406A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.809A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.715A pdb=" N LEU H 11 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA H 13 " --> pdb=" O ASP H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.743A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU H 33 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.661A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER H 131 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU H 181 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL H 133 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU H 179 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU H 135 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER H 177 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.567A pdb=" N TRP H 148 " --> pdb=" O LYS H 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 135 through 145 current: chain 'I' and resid 176 through 185 Processing sheet with id=AE3, first strand: chain 'I' and resid 151 through 154 removed outlier: 4.389A pdb=" N TYR I 194 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.742A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.691A pdb=" N LEU J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA J 13 " --> pdb=" O ASP J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.744A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU J 33 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.664A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER J 131 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU J 181 " --> pdb=" O SER J 131 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL J 133 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU J 179 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU J 135 " --> pdb=" O SER J 177 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER J 177 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN J 137 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU J 175 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'K' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 13 current: chain 'K' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 102 through 103 Processing sheet with id=AF2, first strand: chain 'K' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 135 through 145 current: chain 'K' and resid 176 through 185 Processing sheet with id=AF3, first strand: chain 'K' and resid 151 through 154 removed outlier: 4.405A pdb=" N TYR K 194 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.629A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.412A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.692A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 153 through 154 738 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7725 1.34 - 1.47: 6345 1.47 - 1.59: 10980 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 25227 Sorted by residual: bond pdb=" CB ASN I 29 " pdb=" CG ASN I 29 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.48e+00 bond pdb=" CG ASN I 29 " pdb=" ND2 ASN I 29 " ideal model delta sigma weight residual 1.328 1.373 -0.045 2.10e-02 2.27e+03 4.51e+00 bond pdb=" CA ASN G 76 " pdb=" CB ASN G 76 " ideal model delta sigma weight residual 1.530 1.558 -0.028 1.48e-02 4.57e+03 3.59e+00 bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 33707 2.12 - 4.24: 509 4.24 - 6.36: 65 6.36 - 8.48: 8 8.48 - 10.60: 1 Bond angle restraints: 34290 Sorted by residual: angle pdb=" CB LYS L 169 " pdb=" CG LYS L 169 " pdb=" CD LYS L 169 " ideal model delta sigma weight residual 111.30 121.90 -10.60 2.30e+00 1.89e-01 2.12e+01 angle pdb=" C SER I 28 " pdb=" N ASN I 29 " pdb=" CA ASN I 29 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N VAL F 513 " pdb=" CA VAL F 513 " pdb=" C VAL F 513 " ideal model delta sigma weight residual 111.62 108.76 2.86 7.90e-01 1.60e+00 1.31e+01 angle pdb=" CA ASN G 76 " pdb=" CB ASN G 76 " pdb=" CG ASN G 76 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ARG I 38 " pdb=" CB ARG I 38 " pdb=" CG ARG I 38 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.35e+00 ... (remaining 34285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14323 17.98 - 35.95: 1450 35.95 - 53.93: 399 53.93 - 71.91: 112 71.91 - 89.89: 21 Dihedral angle restraints: 16305 sinusoidal: 7521 harmonic: 8784 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -147.12 61.12 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 201 " pdb=" SG CYS A 201 " pdb=" SG CYS A 433 " pdb=" CB CYS A 433 " ideal model delta sinusoidal sigma weight residual -86.00 -146.83 60.83 1 1.00e+01 1.00e-02 4.92e+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 -144.45 58.45 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 16302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3982 0.108 - 0.215: 190 0.215 - 0.323: 0 0.323 - 0.431: 2 0.431 - 0.538: 2 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 363 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" C1 NAG p 1 " pdb=" ND2 ASN E 363 " pdb=" C2 NAG p 1 " pdb=" O5 NAG p 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 355 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4173 not shown) Planarity restraints: 4302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 116 " 0.016 2.00e-02 2.50e+03 2.10e-02 7.75e+00 pdb=" CG PHE H 116 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE H 116 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE H 116 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE H 116 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 116 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 116 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 76 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C ASN G 76 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN G 76 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 77 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " -0.186 9.50e-02 1.11e+02 8.37e-02 5.15e+00 pdb=" NE ARG A 444 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " -0.001 2.00e-02 2.50e+03 ... (remaining 4299 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 188 2.61 - 3.18: 20296 3.18 - 3.76: 37136 3.76 - 4.33: 53274 4.33 - 4.90: 88204 Nonbonded interactions: 199098 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.038 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR E 139 " pdb=" OD1 ASP E 141 " model vdw 2.147 3.040 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR D 606 " model vdw 2.148 3.040 ... (remaining 199093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' 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 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 8.290 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.360 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.064 25362 Z= 0.146 Angle : 0.686 22.393 34647 Z= 0.333 Chirality : 0.046 0.538 4176 Planarity : 0.004 0.084 4254 Dihedral : 15.434 89.887 10485 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.43 % Rotamer: Outliers : 1.08 % Allowed : 18.83 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2994 helix: 1.55 (0.26), residues: 469 sheet: 1.04 (0.15), residues: 1089 loop : -0.22 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 444 TYR 0.030 0.001 TYR I 33 PHE 0.047 0.001 PHE H 116 TRP 0.016 0.001 TRP B 571 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00329 (25227) covalent geometry : angle 0.63310 (34290) SS BOND : bond 0.00306 ( 48) SS BOND : angle 1.14306 ( 96) hydrogen bonds : bond 0.11888 ( 738) hydrogen bonds : angle 5.76672 ( 1980) link_ALPHA1-2 : bond 0.00440 ( 3) link_ALPHA1-2 : angle 1.61456 ( 9) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 1.59096 ( 9) link_BETA1-4 : bond 0.00383 ( 33) link_BETA1-4 : angle 1.30468 ( 99) link_NAG-ASN : bond 0.00540 ( 48) link_NAG-ASN : angle 3.91216 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: A 194 ILE cc_start: 0.8969 (tp) cc_final: 0.8638 (pt) REVERT: E 166 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7673 (ttp80) REVERT: E 236 THR cc_start: 0.8646 (m) cc_final: 0.8263 (m) REVERT: G 178 LEU cc_start: 0.1672 (pp) cc_final: 0.1285 (pt) REVERT: H 47 LEU cc_start: 0.8119 (mt) cc_final: 0.7860 (mt) REVERT: J 87 PHE cc_start: 0.5197 (p90) cc_final: 0.4970 (p90) REVERT: L 30 ASP cc_start: 0.7566 (t0) cc_final: 0.6519 (m-30) REVERT: L 82 ASP cc_start: 0.6164 (m-30) cc_final: 0.5642 (t0) outliers start: 29 outliers final: 20 residues processed: 264 average time/residue: 0.6966 time to fit residues: 210.5478 Evaluate side-chains 238 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ARG Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 213 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 591 GLN B 607 ASN B 656 ASN C 103 GLN C 280 ASN D 658 GLN E 33 ASN F 653 GLN G 58 ASN I 29 ASN I 58 ASN J 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.219135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162010 restraints weight = 28482.998| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.98 r_work: 0.3358 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25362 Z= 0.212 Angle : 0.703 17.459 34647 Z= 0.332 Chirality : 0.048 0.515 4176 Planarity : 0.004 0.049 4254 Dihedral : 7.910 59.793 5077 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Rotamer: Outliers : 3.54 % Allowed : 16.74 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2994 helix: 1.08 (0.25), residues: 473 sheet: 1.04 (0.16), residues: 1044 loop : -0.28 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 444 TYR 0.017 0.002 TYR C 486 PHE 0.029 0.002 PHE J 94 TRP 0.015 0.002 TRP A 96 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00505 (25227) covalent geometry : angle 0.65053 (34290) SS BOND : bond 0.00497 ( 48) SS BOND : angle 1.11379 ( 96) hydrogen bonds : bond 0.04337 ( 738) hydrogen bonds : angle 5.00623 ( 1980) link_ALPHA1-2 : bond 0.00415 ( 3) link_ALPHA1-2 : angle 1.62816 ( 9) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 1.52704 ( 9) link_BETA1-4 : bond 0.00514 ( 33) link_BETA1-4 : angle 1.50665 ( 99) link_NAG-ASN : bond 0.00614 ( 48) link_NAG-ASN : angle 3.93560 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 226 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8345 (tt0) cc_final: 0.8134 (tt0) REVERT: A 153 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: A 308 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8038 (mtp85) REVERT: C 500 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8014 (mtt-85) REVERT: D 634 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: G 170 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4542 (pp) REVERT: G 178 LEU cc_start: 0.1507 (pp) cc_final: 0.1180 (pt) REVERT: H 33 LEU cc_start: 0.8259 (tt) cc_final: 0.8019 (tt) REVERT: H 47 LEU cc_start: 0.8195 (mt) cc_final: 0.7991 (mt) REVERT: J 87 PHE cc_start: 0.4801 (p90) cc_final: 0.4497 (p90) REVERT: L 2 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6200 (tt) REVERT: L 23 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6578 (t) REVERT: L 30 ASP cc_start: 0.7644 (t0) cc_final: 0.6598 (m-30) outliers start: 95 outliers final: 36 residues processed: 304 average time/residue: 0.6429 time to fit residues: 226.6028 Evaluate side-chains 251 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 224 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 211 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 591 GLN E 33 ASN H 6 GLN I 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162792 restraints weight = 28428.588| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.79 r_work: 0.3353 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25362 Z= 0.159 Angle : 0.617 13.522 34647 Z= 0.293 Chirality : 0.045 0.508 4176 Planarity : 0.004 0.046 4254 Dihedral : 6.866 59.925 5051 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 2.91 % Allowed : 17.97 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 2994 helix: 1.10 (0.26), residues: 473 sheet: 1.04 (0.16), residues: 1044 loop : -0.31 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 588 TYR 0.011 0.001 TYR C 173 PHE 0.021 0.002 PHE J 94 TRP 0.016 0.001 TRP C 427 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00379 (25227) covalent geometry : angle 0.56704 (34290) SS BOND : bond 0.00382 ( 48) SS BOND : angle 0.89463 ( 96) hydrogen bonds : bond 0.03852 ( 738) hydrogen bonds : angle 4.83888 ( 1980) link_ALPHA1-2 : bond 0.00315 ( 3) link_ALPHA1-2 : angle 1.64088 ( 9) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 1.40884 ( 9) link_BETA1-4 : bond 0.00445 ( 33) link_BETA1-4 : angle 1.30474 ( 99) link_NAG-ASN : bond 0.00464 ( 48) link_NAG-ASN : angle 3.61801 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7389 (t) cc_final: 0.7032 (t) REVERT: A 92 GLU cc_start: 0.8391 (tt0) cc_final: 0.8175 (tt0) REVERT: A 153 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: A 308 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8107 (mtp85) REVERT: B 588 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.6183 (ttm170) REVERT: C 87 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: C 151 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8029 (mtm180) REVERT: G 170 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4502 (pp) REVERT: G 178 LEU cc_start: 0.1905 (pp) cc_final: 0.1526 (pt) REVERT: H 33 LEU cc_start: 0.8306 (tt) cc_final: 0.7952 (tt) REVERT: J 87 PHE cc_start: 0.4816 (p90) cc_final: 0.4553 (p90) outliers start: 78 outliers final: 38 residues processed: 281 average time/residue: 0.6637 time to fit residues: 215.6578 Evaluate side-chains 248 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 591 GLN C 137 ASN E 33 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.219227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131832 restraints weight = 28269.639| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.81 r_work: 0.2888 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25362 Z= 0.181 Angle : 0.628 13.560 34647 Z= 0.297 Chirality : 0.046 0.506 4176 Planarity : 0.004 0.046 4254 Dihedral : 6.405 55.616 5048 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 3.73 % Allowed : 17.45 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2994 helix: 1.14 (0.26), residues: 461 sheet: 0.91 (0.16), residues: 1062 loop : -0.33 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 444 TYR 0.010 0.001 TYR G 99 PHE 0.016 0.002 PHE E 383 TRP 0.018 0.002 TRP C 427 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00437 (25227) covalent geometry : angle 0.57762 (34290) SS BOND : bond 0.00424 ( 48) SS BOND : angle 1.07009 ( 96) hydrogen bonds : bond 0.03937 ( 738) hydrogen bonds : angle 4.78502 ( 1980) link_ALPHA1-2 : bond 0.00327 ( 3) link_ALPHA1-2 : angle 1.65998 ( 9) link_ALPHA1-3 : bond 0.01145 ( 3) link_ALPHA1-3 : angle 1.38078 ( 9) link_BETA1-4 : bond 0.00450 ( 33) link_BETA1-4 : angle 1.37736 ( 99) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 3.62820 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 211 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 153 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: A 308 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8202 (mtp85) REVERT: B 542 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8537 (ptm160) REVERT: B 652 GLN cc_start: 0.7100 (tt0) cc_final: 0.6772 (mt0) REVERT: C 87 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: C 121 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8445 (ttmt) REVERT: C 151 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7772 (mtm180) REVERT: C 327 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8024 (ptt-90) REVERT: C 500 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8370 (mtt-85) REVERT: E 107 ASP cc_start: 0.9074 (m-30) cc_final: 0.8847 (m-30) REVERT: E 430 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8564 (mm) REVERT: G 170 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.4835 (pp) REVERT: G 178 LEU cc_start: 0.1969 (pp) cc_final: 0.1644 (pt) REVERT: H 33 LEU cc_start: 0.8304 (tt) cc_final: 0.7923 (tt) REVERT: J 32 ASP cc_start: 0.5350 (m-30) cc_final: 0.4649 (p0) REVERT: J 87 PHE cc_start: 0.4233 (p90) cc_final: 0.3953 (p90) outliers start: 100 outliers final: 51 residues processed: 294 average time/residue: 0.6614 time to fit residues: 224.5257 Evaluate side-chains 260 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 294 optimal weight: 0.0980 chunk 216 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 215 optimal weight: 0.0050 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 591 GLN B 640 GLN E 33 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.220414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133479 restraints weight = 28269.779| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.81 r_work: 0.2910 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25362 Z= 0.126 Angle : 0.576 12.917 34647 Z= 0.274 Chirality : 0.044 0.486 4176 Planarity : 0.003 0.043 4254 Dihedral : 5.836 53.593 5047 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 3.17 % Allowed : 18.68 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2994 helix: 1.32 (0.26), residues: 461 sheet: 1.14 (0.16), residues: 1056 loop : -0.37 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 444 TYR 0.009 0.001 TYR C 173 PHE 0.014 0.001 PHE H 87 TRP 0.018 0.001 TRP C 427 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00294 (25227) covalent geometry : angle 0.52574 (34290) SS BOND : bond 0.00601 ( 48) SS BOND : angle 0.94271 ( 96) hydrogen bonds : bond 0.03509 ( 738) hydrogen bonds : angle 4.65776 ( 1980) link_ALPHA1-2 : bond 0.00293 ( 3) link_ALPHA1-2 : angle 1.65352 ( 9) link_ALPHA1-3 : bond 0.01169 ( 3) link_ALPHA1-3 : angle 1.25872 ( 9) link_BETA1-4 : bond 0.00422 ( 33) link_BETA1-4 : angle 1.28768 ( 99) link_NAG-ASN : bond 0.00470 ( 48) link_NAG-ASN : angle 3.48158 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 206 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8538 (tt0) cc_final: 0.8310 (tt0) REVERT: A 308 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8221 (mtp85) REVERT: B 588 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.5923 (ttm170) REVERT: B 652 GLN cc_start: 0.7128 (tt0) cc_final: 0.6820 (mt0) REVERT: C 151 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7778 (mtm180) REVERT: C 327 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8204 (ptt90) REVERT: C 500 ARG cc_start: 0.8668 (mtp85) cc_final: 0.8393 (mtt-85) REVERT: E 430 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8529 (mm) REVERT: G 170 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4843 (pp) REVERT: G 178 LEU cc_start: 0.1959 (pp) cc_final: 0.1647 (pt) REVERT: H 33 LEU cc_start: 0.8304 (tt) cc_final: 0.7902 (tt) REVERT: J 32 ASP cc_start: 0.5391 (m-30) cc_final: 0.4757 (p0) REVERT: J 87 PHE cc_start: 0.4167 (p90) cc_final: 0.3926 (p90) outliers start: 85 outliers final: 48 residues processed: 278 average time/residue: 0.6602 time to fit residues: 211.0971 Evaluate side-chains 256 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 36 optimal weight: 4.9990 chunk 188 optimal weight: 30.0000 chunk 20 optimal weight: 0.4980 chunk 171 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 277 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 260 optimal weight: 20.0000 chunk 289 optimal weight: 7.9990 overall best weight: 0.7150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN C 136 ASN E 33 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN J 6 GLN L 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.218379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157309 restraints weight = 28336.534| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.96 r_work: 0.3323 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25362 Z= 0.117 Angle : 0.566 12.725 34647 Z= 0.269 Chirality : 0.044 0.463 4176 Planarity : 0.003 0.042 4254 Dihedral : 5.371 47.484 5044 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 3.28 % Allowed : 18.90 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2994 helix: 1.39 (0.26), residues: 461 sheet: 1.18 (0.16), residues: 1053 loop : -0.35 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 444 TYR 0.010 0.001 TYR A 173 PHE 0.013 0.001 PHE H 87 TRP 0.015 0.001 TRP C 427 HIS 0.002 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00274 (25227) covalent geometry : angle 0.51714 (34290) SS BOND : bond 0.00315 ( 48) SS BOND : angle 0.90211 ( 96) hydrogen bonds : bond 0.03378 ( 738) hydrogen bonds : angle 4.58078 ( 1980) link_ALPHA1-2 : bond 0.00330 ( 3) link_ALPHA1-2 : angle 1.64731 ( 9) link_ALPHA1-3 : bond 0.01115 ( 3) link_ALPHA1-3 : angle 1.18692 ( 9) link_BETA1-4 : bond 0.00418 ( 33) link_BETA1-4 : angle 1.27628 ( 99) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 3.38511 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 212 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8268 (tt0) cc_final: 0.8042 (tt0) REVERT: A 153 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: A 308 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8012 (mtp85) REVERT: B 588 ARG cc_start: 0.7647 (tpp-160) cc_final: 0.6018 (ttm170) REVERT: C 87 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: C 151 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7997 (mtm180) REVERT: C 327 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8162 (ptt90) REVERT: C 500 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8104 (mtt180) REVERT: E 430 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8531 (mm) REVERT: G 170 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4558 (pp) REVERT: G 178 LEU cc_start: 0.2187 (pp) cc_final: 0.1830 (pt) REVERT: H 33 LEU cc_start: 0.8325 (tt) cc_final: 0.7946 (tt) REVERT: J 32 ASP cc_start: 0.5677 (m-30) cc_final: 0.4997 (p0) outliers start: 88 outliers final: 54 residues processed: 286 average time/residue: 0.6233 time to fit residues: 205.8596 Evaluate side-chains 264 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 271 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN B 607 ASN B 640 GLN B 658 GLN C 136 ASN C 300 ASN E 33 ASN F 543 ASN G 164 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN J 166 GLN L 3 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.215289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153227 restraints weight = 28234.681| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.93 r_work: 0.3313 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25362 Z= 0.215 Angle : 0.657 13.949 34647 Z= 0.310 Chirality : 0.047 0.524 4176 Planarity : 0.004 0.042 4254 Dihedral : 5.523 48.968 5044 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.47 % Allowed : 19.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2994 helix: 1.01 (0.25), residues: 461 sheet: 1.04 (0.16), residues: 1020 loop : -0.41 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 444 TYR 0.013 0.001 TYR G 99 PHE 0.018 0.002 PHE H 87 TRP 0.018 0.002 TRP C 427 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00527 (25227) covalent geometry : angle 0.60560 (34290) SS BOND : bond 0.00437 ( 48) SS BOND : angle 1.12160 ( 96) hydrogen bonds : bond 0.04200 ( 738) hydrogen bonds : angle 4.76393 ( 1980) link_ALPHA1-2 : bond 0.00349 ( 3) link_ALPHA1-2 : angle 1.71435 ( 9) link_ALPHA1-3 : bond 0.01013 ( 3) link_ALPHA1-3 : angle 1.26995 ( 9) link_BETA1-4 : bond 0.00432 ( 33) link_BETA1-4 : angle 1.42964 ( 99) link_NAG-ASN : bond 0.00596 ( 48) link_NAG-ASN : angle 3.75147 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 209 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 95 MET cc_start: 0.8989 (ttp) cc_final: 0.8775 (ttp) REVERT: A 153 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 217 TYR cc_start: 0.8742 (m-80) cc_final: 0.8520 (m-80) REVERT: A 308 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8107 (mtp85) REVERT: B 542 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.8448 (ptm160) REVERT: B 619 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8114 (mp) REVERT: C 87 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: C 121 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8321 (ttmt) REVERT: C 151 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.8035 (mtm180) REVERT: C 232 LYS cc_start: 0.8163 (mtmp) cc_final: 0.7913 (mtpt) REVERT: C 327 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7985 (ptt-90) REVERT: C 500 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8113 (mtt-85) REVERT: E 107 ASP cc_start: 0.8980 (m-30) cc_final: 0.8715 (m-30) REVERT: F 621 GLU cc_start: 0.8237 (pt0) cc_final: 0.7668 (mm-30) REVERT: G 170 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4605 (pp) REVERT: G 178 LEU cc_start: 0.2151 (pp) cc_final: 0.1830 (pt) REVERT: H 169 LYS cc_start: 0.4900 (mmtt) cc_final: 0.4179 (ptmt) REVERT: J 32 ASP cc_start: 0.5702 (m-30) cc_final: 0.5043 (p0) outliers start: 93 outliers final: 64 residues processed: 287 average time/residue: 0.6014 time to fit residues: 198.5480 Evaluate side-chains 260 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 13 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 30 optimal weight: 0.0970 chunk 250 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 136 ASN A 137 ASN B 591 GLN B 640 GLN C 103 GLN C 136 ASN E 33 ASN E 82 GLN H 3 GLN I 29 ASN L 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.218097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160811 restraints weight = 28359.661| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.81 r_work: 0.3395 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25362 Z= 0.104 Angle : 0.574 12.766 34647 Z= 0.273 Chirality : 0.044 0.465 4176 Planarity : 0.003 0.041 4254 Dihedral : 5.126 48.477 5044 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.68 % Allowed : 20.10 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2994 helix: 1.32 (0.26), residues: 461 sheet: 1.07 (0.16), residues: 1092 loop : -0.31 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 444 TYR 0.010 0.001 TYR C 173 PHE 0.014 0.001 PHE J 71 TRP 0.020 0.001 TRP E 427 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00237 (25227) covalent geometry : angle 0.52569 (34290) SS BOND : bond 0.00345 ( 48) SS BOND : angle 0.89902 ( 96) hydrogen bonds : bond 0.03317 ( 738) hydrogen bonds : angle 4.55702 ( 1980) link_ALPHA1-2 : bond 0.00309 ( 3) link_ALPHA1-2 : angle 1.63394 ( 9) link_ALPHA1-3 : bond 0.01095 ( 3) link_ALPHA1-3 : angle 1.06303 ( 9) link_BETA1-4 : bond 0.00395 ( 33) link_BETA1-4 : angle 1.26429 ( 99) link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 3.41867 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 201 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8315 (tt0) cc_final: 0.8097 (tt0) REVERT: A 95 MET cc_start: 0.8838 (ttp) cc_final: 0.8601 (ttp) REVERT: A 153 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: A 308 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7965 (mtp85) REVERT: C 327 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8091 (ptt90) REVERT: C 500 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8060 (mtt180) REVERT: F 621 GLU cc_start: 0.8034 (pt0) cc_final: 0.7423 (mt-10) REVERT: G 170 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4501 (pp) REVERT: G 178 LEU cc_start: 0.2261 (pp) cc_final: 0.1918 (pt) REVERT: J 32 ASP cc_start: 0.5660 (m-30) cc_final: 0.4993 (p0) outliers start: 72 outliers final: 44 residues processed: 263 average time/residue: 0.6306 time to fit residues: 190.3917 Evaluate side-chains 240 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN B 607 ASN C 103 GLN C 136 ASN E 33 ASN E 377 ASN F 543 ASN I 29 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132433 restraints weight = 28301.630| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.77 r_work: 0.2857 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25362 Z= 0.207 Angle : 0.653 13.615 34647 Z= 0.310 Chirality : 0.047 0.504 4176 Planarity : 0.004 0.042 4254 Dihedral : 5.307 48.881 5043 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.80 % Allowed : 20.10 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2994 helix: 1.07 (0.26), residues: 461 sheet: 0.92 (0.16), residues: 1059 loop : -0.34 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 444 TYR 0.015 0.001 TYR A 435 PHE 0.018 0.002 PHE H 87 TRP 0.016 0.002 TRP C 427 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00507 (25227) covalent geometry : angle 0.60532 (34290) SS BOND : bond 0.00463 ( 48) SS BOND : angle 1.06917 ( 96) hydrogen bonds : bond 0.04064 ( 738) hydrogen bonds : angle 4.69461 ( 1980) link_ALPHA1-2 : bond 0.00361 ( 3) link_ALPHA1-2 : angle 1.66883 ( 9) link_ALPHA1-3 : bond 0.00975 ( 3) link_ALPHA1-3 : angle 1.18333 ( 9) link_BETA1-4 : bond 0.00412 ( 33) link_BETA1-4 : angle 1.40119 ( 99) link_NAG-ASN : bond 0.00596 ( 48) link_NAG-ASN : angle 3.60704 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 194 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: A 308 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8300 (mtp85) REVERT: B 542 ARG cc_start: 0.8780 (ptp-110) cc_final: 0.8571 (ptm160) REVERT: C 232 LYS cc_start: 0.8123 (mtmp) cc_final: 0.7870 (mtpt) REVERT: C 327 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (ptt-90) REVERT: C 500 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8385 (mtt-85) REVERT: F 621 GLU cc_start: 0.8497 (pt0) cc_final: 0.7596 (mm-30) REVERT: G 170 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5055 (pp) REVERT: J 32 ASP cc_start: 0.5117 (m-30) cc_final: 0.4529 (p0) outliers start: 75 outliers final: 51 residues processed: 258 average time/residue: 0.6570 time to fit residues: 195.2138 Evaluate side-chains 240 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 60 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 196 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 137 ASN B 591 GLN B 607 ASN B 658 GLN C 103 GLN C 136 ASN E 33 ASN E 377 ASN I 29 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.218556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133076 restraints weight = 28335.810| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.48 r_work: 0.2934 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25362 Z= 0.150 Angle : 0.619 16.972 34647 Z= 0.292 Chirality : 0.046 0.489 4176 Planarity : 0.004 0.057 4254 Dihedral : 5.235 52.951 5043 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.50 % Allowed : 20.43 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2994 helix: 1.17 (0.26), residues: 461 sheet: 0.95 (0.16), residues: 1053 loop : -0.32 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 444 TYR 0.012 0.001 TYR A 435 PHE 0.016 0.001 PHE L 87 TRP 0.018 0.001 TRP C 427 HIS 0.003 0.000 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00357 (25227) covalent geometry : angle 0.56227 (34290) SS BOND : bond 0.00395 ( 48) SS BOND : angle 0.94924 ( 96) hydrogen bonds : bond 0.03670 ( 738) hydrogen bonds : angle 4.63421 ( 1980) link_ALPHA1-2 : bond 0.00342 ( 3) link_ALPHA1-2 : angle 1.65451 ( 9) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 1.09229 ( 9) link_BETA1-4 : bond 0.00388 ( 33) link_BETA1-4 : angle 1.35363 ( 99) link_NAG-ASN : bond 0.00475 ( 48) link_NAG-ASN : angle 3.85098 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: A 308 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: B 542 ARG cc_start: 0.8770 (ptp-110) cc_final: 0.8554 (ptm160) REVERT: C 83 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7440 (tm-30) REVERT: C 232 LYS cc_start: 0.8075 (mtmp) cc_final: 0.7843 (mtpt) REVERT: C 327 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8023 (ptt-90) REVERT: C 500 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8376 (mtt-85) REVERT: E 308 ARG cc_start: 0.8991 (mtt-85) cc_final: 0.8745 (mtp85) REVERT: F 621 GLU cc_start: 0.8420 (pt0) cc_final: 0.7558 (mt-10) REVERT: G 170 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.5067 (pp) REVERT: J 32 ASP cc_start: 0.5062 (m-30) cc_final: 0.4506 (p0) outliers start: 67 outliers final: 53 residues processed: 251 average time/residue: 0.6520 time to fit residues: 187.8718 Evaluate side-chains 246 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 72 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 136 ASN A 137 ASN B 591 GLN B 607 ASN B 640 GLN C 103 GLN C 136 ASN E 33 ASN E 82 GLN E 377 ASN F 543 ASN I 29 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.218687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134664 restraints weight = 28268.576| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.03 r_work: 0.2984 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25362 Z= 0.146 Angle : 0.625 21.391 34647 Z= 0.293 Chirality : 0.045 0.479 4176 Planarity : 0.004 0.052 4254 Dihedral : 5.208 59.261 5043 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.61 % Allowed : 20.25 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2994 helix: 1.19 (0.26), residues: 461 sheet: 1.01 (0.16), residues: 1083 loop : -0.34 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 444 TYR 0.012 0.001 TYR A 435 PHE 0.016 0.001 PHE H 87 TRP 0.020 0.001 TRP E 427 HIS 0.003 0.000 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00348 (25227) covalent geometry : angle 0.56257 (34290) SS BOND : bond 0.00385 ( 48) SS BOND : angle 0.92592 ( 96) hydrogen bonds : bond 0.03623 ( 738) hydrogen bonds : angle 4.61163 ( 1980) link_ALPHA1-2 : bond 0.00331 ( 3) link_ALPHA1-2 : angle 1.63633 ( 9) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.09490 ( 9) link_BETA1-4 : bond 0.00396 ( 33) link_BETA1-4 : angle 1.38056 ( 99) link_NAG-ASN : bond 0.00477 ( 48) link_NAG-ASN : angle 4.04726 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11454.42 seconds wall clock time: 195 minutes 23.15 seconds (11723.15 seconds total)