Starting phenix.real_space_refine on Fri Aug 7 06:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkc_41346/08_2026/8tkc_41346.map" } resolution = 3.1 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= 0.041 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 123 5.16 5 C 12549 2.51 5 N 3336 2.21 5 O 4056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20064 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: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.45, per 1000 atoms: 0.22 Number of scatterers: 20064 At special positions: 0 Unit cell: (150.284, 142.51, 124.373, 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 123 16.00 O 4056 8.00 N 3336 7.00 C 12549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 743.9 milliseconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 41 sheets defined 19.0% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.122A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.597A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.253A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.882A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.595A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.887A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.724A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.162A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.551A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.920A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 521 through 527 removed outlier: 4.595A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.985A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.729A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.178A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.547A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.505A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 527 removed outlier: 4.549A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.088A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.552A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.903A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.750A 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 'H' and resid 79 through 83 removed outlier: 3.869A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.863A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.860A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.039A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.567A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.398A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.051A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.600A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.186A pdb=" N GLY B 516 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.596A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.311A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.831A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.032A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.581A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 517 through 519 removed outlier: 6.646A pdb=" N VAL D 518 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.600A pdb=" N VAL I 12 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.293A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.065A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.418A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.030A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.506A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'F' and resid 517 through 519 removed outlier: 6.737A pdb=" N VAL F 518 " --> pdb=" O TYR K 99 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR K 34 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.605A pdb=" N VAL K 12 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.536A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.538A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.539A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 1974 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: 3.62 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.26: 3199 1.26 - 1.61: 17107 1.61 - 1.97: 162 1.97 - 2.32: 0 2.32 - 2.67: 1 Bond restraints: 20469 Sorted by residual: bond pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 1.492 2.675 -1.183 5.00e-02 4.00e+02 5.60e+02 bond pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.503 0.908 0.595 3.40e-02 8.65e+02 3.06e+02 bond pdb=" C ALA A 497 " pdb=" N PRO A 498 " ideal model delta sigma weight residual 1.329 1.420 -0.090 1.25e-02 6.40e+03 5.22e+01 bond pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 1.534 1.454 0.080 1.23e-02 6.61e+03 4.22e+01 bond pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.473 1.563 -0.090 1.40e-02 5.10e+03 4.17e+01 ... (remaining 20464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.92: 27806 19.92 - 39.84: 0 39.84 - 59.76: 0 59.76 - 79.68: 0 79.68 - 99.60: 1 Bond angle restraints: 27807 Sorted by residual: angle pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 106.10 6.50 99.60 3.20e+00 9.77e-02 9.69e+02 angle pdb=" N PRO A 498 " pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 103.15 92.10 11.05 9.70e-01 1.06e+00 1.30e+02 angle pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 104.50 87.00 17.50 1.90e+00 2.77e-01 8.48e+01 angle pdb=" CA PRO A 498 " pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 132.09 -17.69 2.30e+00 1.89e-01 5.92e+01 ... (remaining 27802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12513 27.42 - 54.84: 686 54.84 - 82.26: 114 82.26 - 109.68: 42 109.68 - 137.10: 1 Dihedral angle restraints: 13356 sinusoidal: 6408 harmonic: 6948 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.18 87.82 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 26.04 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -21.97 -64.03 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2891 0.062 - 0.124: 403 0.124 - 0.187: 70 0.187 - 0.249: 2 0.249 - 0.311: 12 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA CYS E 296 " pdb=" N CYS E 296 " pdb=" C CYS E 296 " pdb=" CB CYS E 296 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3375 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO C 240 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 100F" -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO I 100G" 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 100G" -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 100F" -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 100G" 0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 100G" -0.031 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 396 2.69 - 3.24: 17654 3.24 - 3.79: 28755 3.79 - 4.35: 39112 4.35 - 4.90: 67608 Nonbonded interactions: 153525 Sorted by model distance: nonbonded pdb=" OG1 THR A 139 " pdb=" OD1 ASP A 141 " model vdw 2.134 3.040 nonbonded pdb=" O PHE D 522 " pdb=" NE2 GLN D 540 " model vdw 2.188 3.120 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.194 3.040 nonbonded pdb=" O ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.223 3.040 ... (remaining 153520 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.140 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.011 1.183 20598 Z= 0.316 Angle : 0.974 99.605 28152 Z= 0.417 Chirality : 0.049 0.311 3378 Planarity : 0.004 0.060 3429 Dihedral : 16.986 137.102 8754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 0.33 % Allowed : 13.44 % Favored : 86.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.00 (0.17), residues: 2373 helix: 2.24 (0.29), residues: 396 sheet: 0.15 (0.18), residues: 777 loop : -0.87 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 444 TYR 0.036 0.001 TYR I 34 PHE 0.010 0.001 PHE A 53 TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.01055 / 0.32 (20469) covalent geometry : angle 0.95417 / 0.41 (27807) SS BOND : bond 0.00678 / 0.47 ( 42) SS BOND : angle 2.56207 / 1.67 ( 84) hydrogen bonds : bond 0.10911 / 7.57 ( 735) hydrogen bonds : angle 5.34300 / 3.79 ( 1974) link_ALPHA1-2 : bond 0.00321 / 0.15 ( 3) link_ALPHA1-2 : angle 1.60373 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00556 / 0.25 ( 3) link_ALPHA1-3 : angle 1.46490 / 0.88 ( 9) link_BETA1-4 : bond 0.00480 / 0.30 ( 36) link_BETA1-4 : angle 1.01362 / 0.67 ( 108) link_NAG-ASN : bond 0.00307 / 0.19 ( 45) link_NAG-ASN : angle 2.23787 / 1.55 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLU cc_start: 0.7880 (tp30) cc_final: 0.7666 (tp30) REVERT: C 268 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6719 (pm20) REVERT: E 268 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6634 (pm20) REVERT: E 475 MET cc_start: 0.8836 (mmp) cc_final: 0.8611 (tpp) REVERT: F 655 LYS cc_start: 0.6394 (ttpt) cc_final: 0.5968 (ttpt) outliers start: 7 outliers final: 5 residues processed: 182 average time/residue: 0.1825 time to fit residues: 47.2590 Evaluate side-chains 175 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain I residue 100 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 235 optimal weight: 20.0000 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 653 GLN E 137 ASN E 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.208587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137792 restraints weight = 20813.893| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.49 r_work: 0.3176 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.022 20598 Z= 0.257 Angle : 0.934 106.098 28152 Z= 0.400 Chirality : 0.044 0.251 3378 Planarity : 0.004 0.068 3429 Dihedral : 12.797 101.818 4377 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 0.66 % Allowed : 14.05 % Favored : 85.29 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % 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: 0.08 (0.17), residues: 2373 helix: 2.41 (0.29), residues: 399 sheet: 0.17 (0.18), residues: 783 loop : -0.84 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 444 TYR 0.013 0.001 TYR I 34 PHE 0.013 0.001 PHE A 383 TRP 0.006 0.001 TRP D 628 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.25 (20469) covalent geometry : angle 0.91361 / 0.39 (27807) SS BOND : bond 0.01478 / 0.83 ( 42) SS BOND : angle 1.81031 / 1.13 ( 84) hydrogen bonds : bond 0.05433 / 3.74 ( 735) hydrogen bonds : angle 4.96126 / 3.47 ( 1974) link_ALPHA1-2 : bond 0.01222 / 0.54 ( 3) link_ALPHA1-2 : angle 2.42246 / 1.57 ( 9) link_ALPHA1-3 : bond 0.01208 / 0.54 ( 3) link_ALPHA1-3 : angle 2.17490 / 1.37 ( 9) link_BETA1-4 : bond 0.00721 / 0.47 ( 36) link_BETA1-4 : angle 1.50235 / 1.03 ( 108) link_NAG-ASN : bond 0.00488 / 0.31 ( 45) link_NAG-ASN : angle 2.29704 / 1.60 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8144 (tt0) cc_final: 0.7784 (tt0) REVERT: C 153 GLU cc_start: 0.8034 (tp30) cc_final: 0.7786 (tp30) REVERT: C 178 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7692 (ttp-110) REVERT: C 268 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6632 (pm20) REVERT: E 268 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6585 (pm20) REVERT: E 475 MET cc_start: 0.8828 (mmp) cc_final: 0.8556 (tpp) REVERT: F 655 LYS cc_start: 0.6412 (ttpt) cc_final: 0.6020 (ttpt) outliers start: 14 outliers final: 5 residues processed: 185 average time/residue: 0.1690 time to fit residues: 44.6658 Evaluate side-chains 173 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain J residue 23 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 126 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN C 355 ASN D 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133789 restraints weight = 20925.387| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.91 r_work: 0.3092 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.026 20598 Z= 0.271 Angle : 0.920 106.097 28152 Z= 0.396 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.65 % Allowed : 13.20 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89809 / 0.39 (27807) SS BOND : bond 0.00835 / 0.55 ( 42) SS BOND : angle 2.32052 / 1.36 ( 84) hydrogen bonds : bond 0.04906 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00879 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53673 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10676 / 0.70 ( 9) link_BETA1-4 : bond 0.00719 / 0.45 ( 36) link_BETA1-4 : angle 1.28161 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36346 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8135 (tt0) cc_final: 0.7794 (tt0) REVERT: C 178 ARG cc_start: 0.8173 (tpt90) cc_final: 0.7686 (ttp-110) REVERT: C 268 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6590 (pm20) REVERT: E 268 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 355 ASN cc_start: 0.7325 (t0) cc_final: 0.6942 (t0) REVERT: F 655 LYS cc_start: 0.6466 (ttpt) cc_final: 0.6049 (ttpt) REVERT: L 33 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4615 (tp) outliers start: 35 outliers final: 20 residues processed: 185 average time/residue: 0.1815 time to fit residues: 48.5593 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 125 optimal weight: 0.0770 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.207999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133910 restraints weight = 20899.329| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.91 r_work: 0.3140 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.026 20598 Z= 0.341 Angle : 0.948 106.097 28152 Z= 0.411 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 13.81 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89808 / 0.39 (27807) SS BOND : bond 0.09160 / 5.76 ( 42) SS BOND : angle 4.75958 / 2.72 ( 84) hydrogen bonds : bond 0.04906 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00879 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53676 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10672 / 0.70 ( 9) link_BETA1-4 : bond 0.00719 / 0.45 ( 36) link_BETA1-4 : angle 1.28155 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36346 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8122 (tt0) cc_final: 0.7784 (tt0) REVERT: C 178 ARG cc_start: 0.8181 (tpt90) cc_final: 0.7695 (ttp-110) REVERT: C 268 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6571 (pm20) REVERT: E 268 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6629 (pm20) REVERT: E 355 ASN cc_start: 0.7334 (t0) cc_final: 0.6954 (t0) REVERT: F 655 LYS cc_start: 0.6462 (ttpt) cc_final: 0.6045 (ttpt) REVERT: L 33 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4614 (tp) outliers start: 22 outliers final: 21 residues processed: 173 average time/residue: 0.1850 time to fit residues: 45.3929 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 27 optimal weight: 0.0980 chunk 226 optimal weight: 6.9990 chunk 43 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.8535 > 50:) chunk 72 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.207999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134036 restraints weight = 20793.838| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.85 r_work: 0.3113 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.026 20598 Z= 0.341 Angle : 0.948 106.097 28152 Z= 0.411 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 13.81 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89808 / 0.39 (27807) SS BOND : bond 0.09156 / 5.76 ( 42) SS BOND : angle 4.75910 / 2.72 ( 84) hydrogen bonds : bond 0.04905 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00880 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53678 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10668 / 0.70 ( 9) link_BETA1-4 : bond 0.00718 / 0.45 ( 36) link_BETA1-4 : angle 1.28149 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36346 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8142 (tt0) cc_final: 0.7804 (tt0) REVERT: C 178 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7696 (ttp-110) REVERT: C 268 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6608 (pm20) REVERT: E 268 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6658 (pm20) REVERT: E 355 ASN cc_start: 0.7343 (t0) cc_final: 0.6966 (t0) REVERT: F 655 LYS cc_start: 0.6474 (ttpt) cc_final: 0.6059 (ttpt) REVERT: L 33 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4611 (tp) outliers start: 22 outliers final: 21 residues processed: 173 average time/residue: 0.1845 time to fit residues: 45.7307 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 207 optimal weight: 30.0000 chunk 35 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 108 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.207999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133915 restraints weight = 20778.269| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.89 r_work: 0.3117 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.026 20598 Z= 0.341 Angle : 0.948 106.097 28152 Z= 0.411 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 13.81 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89807 / 0.39 (27807) SS BOND : bond 0.09154 / 5.75 ( 42) SS BOND : angle 4.75877 / 2.72 ( 84) hydrogen bonds : bond 0.04905 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00880 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53679 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10666 / 0.70 ( 9) link_BETA1-4 : bond 0.00718 / 0.45 ( 36) link_BETA1-4 : angle 1.28146 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36345 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8132 (tt0) cc_final: 0.7792 (tt0) REVERT: C 178 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7694 (ttp-110) REVERT: C 268 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6597 (pm20) REVERT: E 268 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6649 (pm20) REVERT: E 355 ASN cc_start: 0.7335 (t0) cc_final: 0.6955 (t0) REVERT: F 655 LYS cc_start: 0.6462 (ttpt) cc_final: 0.6046 (ttpt) REVERT: L 33 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4620 (tp) outliers start: 22 outliers final: 21 residues processed: 173 average time/residue: 0.1935 time to fit residues: 47.4386 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 72 optimal weight: 0.0770 chunk 174 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 221 optimal weight: 20.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.207999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133888 restraints weight = 20891.735| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.92 r_work: 0.3140 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.026 20598 Z= 0.341 Angle : 0.948 106.097 28152 Z= 0.411 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 13.81 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89807 / 0.39 (27807) SS BOND : bond 0.09152 / 5.75 ( 42) SS BOND : angle 4.75854 / 2.72 ( 84) hydrogen bonds : bond 0.04905 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00880 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53680 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10665 / 0.70 ( 9) link_BETA1-4 : bond 0.00718 / 0.45 ( 36) link_BETA1-4 : angle 1.28143 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36345 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8115 (tt0) cc_final: 0.7775 (tt0) REVERT: C 178 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7694 (ttp-110) REVERT: C 268 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6591 (pm20) REVERT: E 268 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6640 (pm20) REVERT: E 355 ASN cc_start: 0.7335 (t0) cc_final: 0.6954 (t0) REVERT: F 655 LYS cc_start: 0.6445 (ttpt) cc_final: 0.6030 (ttpt) REVERT: L 33 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4612 (tp) outliers start: 22 outliers final: 21 residues processed: 173 average time/residue: 0.1847 time to fit residues: 45.3792 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 220 optimal weight: 40.0000 chunk 60 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 99 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.206803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134817 restraints weight = 20785.215| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.82 r_work: 0.3136 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.026 20598 Z= 0.341 Angle : 0.948 106.097 28152 Z= 0.411 Chirality : 0.044 0.245 3378 Planarity : 0.005 0.081 3429 Dihedral : 12.090 95.384 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.04 % Allowed : 13.81 % Favored : 85.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.01 (0.17), residues: 2373 helix: 2.20 (0.28), residues: 399 sheet: 0.22 (0.18), residues: 783 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR C 173 PHE 0.024 0.002 PHE G 100H TRP 0.006 0.001 TRP B 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.27 (20469) covalent geometry : angle 0.89807 / 0.39 (27807) SS BOND : bond 0.09151 / 5.75 ( 42) SS BOND : angle 4.75840 / 2.72 ( 84) hydrogen bonds : bond 0.04905 / 3.32 ( 735) hydrogen bonds : angle 4.87140 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00880 / 0.39 ( 3) link_ALPHA1-2 : angle 1.53681 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01340 / 0.59 ( 3) link_ALPHA1-3 : angle 1.10664 / 0.70 ( 9) link_BETA1-4 : bond 0.00718 / 0.45 ( 36) link_BETA1-4 : angle 1.28142 / 0.88 ( 108) link_NAG-ASN : bond 0.00306 / 0.19 ( 45) link_NAG-ASN : angle 2.36345 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8163 (tt0) cc_final: 0.7827 (tt0) REVERT: C 178 ARG cc_start: 0.8184 (tpt90) cc_final: 0.7723 (ttp-110) REVERT: C 268 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6634 (pm20) REVERT: E 268 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6688 (pm20) REVERT: E 355 ASN cc_start: 0.7353 (t0) cc_final: 0.6978 (t0) REVERT: F 655 LYS cc_start: 0.6506 (ttpt) cc_final: 0.6095 (ttpt) REVERT: L 33 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4572 (tp) outliers start: 22 outliers final: 21 residues processed: 173 average time/residue: 0.1702 time to fit residues: 42.0795 Evaluate side-chains 186 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 177 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.207632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133819 restraints weight = 20846.329| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.82 r_work: 0.3108 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.030 20598 Z= 0.305 Angle : 0.944 106.096 28152 Z= 0.412 Chirality : 0.046 0.250 3378 Planarity : 0.005 0.114 3429 Dihedral : 12.053 95.157 4368 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 1.13 % Allowed : 13.86 % Favored : 85.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.03 (0.17), residues: 2373 helix: 2.12 (0.28), residues: 399 sheet: 0.24 (0.18), residues: 783 loop : -0.94 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 166 TYR 0.012 0.002 TYR C 173 PHE 0.017 0.002 PHE A 383 TRP 0.007 0.001 TRP F 628 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.30 (20469) covalent geometry : angle 0.91500 / 0.40 (27807) SS BOND : bond 0.02090 / 1.26 ( 42) SS BOND : angle 3.19226 / 1.92 ( 84) hydrogen bonds : bond 0.04969 / 3.35 ( 735) hydrogen bonds : angle 4.87184 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00964 / 0.43 ( 3) link_ALPHA1-2 : angle 1.49758 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01316 / 0.59 ( 3) link_ALPHA1-3 : angle 1.16465 / 0.74 ( 9) link_BETA1-4 : bond 0.00768 / 0.49 ( 36) link_BETA1-4 : angle 1.27737 / 0.88 ( 108) link_NAG-ASN : bond 0.00322 / 0.20 ( 45) link_NAG-ASN : angle 2.35635 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8143 (tt0) cc_final: 0.7808 (tt0) REVERT: A 355 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7824 (t0) REVERT: C 178 ARG cc_start: 0.8181 (tpt90) cc_final: 0.7702 (ttp-110) REVERT: C 268 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6616 (pm20) REVERT: E 268 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6656 (pm20) REVERT: E 355 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6956 (t0) REVERT: F 655 LYS cc_start: 0.6489 (ttpt) cc_final: 0.6075 (ttpt) REVERT: L 33 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4597 (tp) outliers start: 24 outliers final: 19 residues processed: 176 average time/residue: 0.1957 time to fit residues: 48.9910 Evaluate side-chains 187 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 147 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.207571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132553 restraints weight = 20945.010| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 4.12 r_work: 0.3108 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.030 20598 Z= 0.302 Angle : 0.946 106.096 28152 Z= 0.413 Chirality : 0.046 0.250 3378 Planarity : 0.005 0.114 3429 Dihedral : 12.053 95.157 4368 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 1.04 % Allowed : 13.91 % Favored : 85.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.03 (0.17), residues: 2373 helix: 2.12 (0.28), residues: 399 sheet: 0.24 (0.18), residues: 783 loop : -0.94 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 166 TYR 0.012 0.002 TYR C 173 PHE 0.017 0.002 PHE A 383 TRP 0.007 0.001 TRP F 628 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.30 (20469) covalent geometry : angle 0.91500 / 0.40 (27807) SS BOND : bond 0.00966 / 0.63 ( 42) SS BOND : angle 3.39020 / 1.98 ( 84) hydrogen bonds : bond 0.04969 / 3.35 ( 735) hydrogen bonds : angle 4.87184 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00964 / 0.43 ( 3) link_ALPHA1-2 : angle 1.49758 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01316 / 0.59 ( 3) link_ALPHA1-3 : angle 1.16465 / 0.74 ( 9) link_BETA1-4 : bond 0.00768 / 0.49 ( 36) link_BETA1-4 : angle 1.27737 / 0.88 ( 108) link_NAG-ASN : bond 0.00322 / 0.20 ( 45) link_NAG-ASN : angle 2.35635 / 1.65 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8087 (tt0) cc_final: 0.7747 (tt0) REVERT: A 355 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7797 (t0) REVERT: C 178 ARG cc_start: 0.8178 (tpt90) cc_final: 0.7674 (ttp-110) REVERT: C 268 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6561 (pm20) REVERT: E 268 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6598 (pm20) REVERT: E 355 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6916 (t0) REVERT: F 655 LYS cc_start: 0.6402 (ttpt) cc_final: 0.5984 (ttpt) REVERT: L 33 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4493 (tp) outliers start: 22 outliers final: 19 residues processed: 173 average time/residue: 0.2048 time to fit residues: 50.1480 Evaluate side-chains 187 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 229 optimal weight: 5.9990 chunk 72 optimal weight: 0.0000 chunk 133 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.207571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132216 restraints weight = 20927.659| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.08 r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.030 20598 Z= 0.302 Angle : 0.946 106.096 28152 Z= 0.413 Chirality : 0.046 0.250 3378 Planarity : 0.005 0.114 3429 Dihedral : 12.053 95.157 4368 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 1.04 % Allowed : 13.91 % Favored : 85.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % 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: -0.03 (0.17), residues: 2373 helix: 2.12 (0.28), residues: 399 sheet: 0.24 (0.18), residues: 783 loop : -0.94 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 166 TYR 0.012 0.002 TYR C 173 PHE 0.017 0.002 PHE A 383 TRP 0.007 0.001 TRP F 628 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.30 (20469) covalent geometry : angle 0.91500 / 0.40 (27807) SS BOND : bond 0.00966 / 0.63 ( 42) SS BOND : angle 3.39020 / 1.98 ( 84) hydrogen bonds : bond 0.04969 / 3.35 ( 735) hydrogen bonds : angle 4.87184 / 3.38 ( 1974) link_ALPHA1-2 : bond 0.00964 / 0.43 ( 3) link_ALPHA1-2 : angle 1.49758 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01316 / 0.59 ( 3) link_ALPHA1-3 : angle 1.16465 / 0.74 ( 9) link_BETA1-4 : bond 0.00768 / 0.49 ( 36) link_BETA1-4 : angle 1.27737 / 0.88 ( 108) link_NAG-ASN : bond 0.00322 / 0.20 ( 45) link_NAG-ASN : angle 2.35635 / 1.65 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5771.67 seconds wall clock time: 99 minutes 14.25 seconds (5954.25 seconds total)