Starting phenix.real_space_refine on Sun Aug 24 14:46:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g30_29686/08_2025/8g30_29686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g30_29686/08_2025/8g30_29686.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/8g30_29686/08_2025/8g30_29686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g30_29686/08_2025/8g30_29686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g30_29686/08_2025/8g30_29686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g30_29686/08_2025/8g30_29686.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= 0.003 sd= 0.053 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12715 2.51 5 N 3422 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20449 Number of models: 1 Model: "" Number of chains: 40 Chain: "E" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2972 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 367} Chain breaks: 1 Chain: "G" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "P" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "a" 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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" 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: "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: "i" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "l" 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: "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: "q" 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: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "v" 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: "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: "1" 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: "2" 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: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "4" 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: "6" 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: "7" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.27 Number of scatterers: 20449 At special positions: 0 Unit cell: (165.933, 165.933, 105.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4191 8.00 N 3422 7.00 C 12715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.06 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 92 " - pdb=" SG CYS M 417 " distance=2.06 Simple disulfide: pdb=" SG CYS M 124 " - pdb=" SG CYS M 129 " distance=2.07 Simple disulfide: pdb=" SG CYS M 175 " - pdb=" SG CYS M 193 " distance=2.01 Simple disulfide: pdb=" SG CYS M 183 " - pdb=" SG CYS M 230 " distance=2.08 Simple disulfide: pdb=" SG CYS M 232 " - pdb=" SG CYS M 237 " distance=2.07 Simple disulfide: pdb=" SG CYS M 278 " - pdb=" SG CYS M 291 " distance=2.01 Simple disulfide: pdb=" SG CYS M 280 " - pdb=" SG CYS M 289 " distance=2.08 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.07 Simple disulfide: pdb=" SG CYS M 421 " - pdb=" SG CYS M 447 " distance=2.09 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.06 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 417 " distance=2.05 Simple disulfide: pdb=" SG CYS N 124 " - pdb=" SG CYS N 129 " distance=2.07 Simple disulfide: pdb=" SG CYS N 175 " - pdb=" SG CYS N 193 " distance=2.01 Simple disulfide: pdb=" SG CYS N 183 " - pdb=" SG CYS N 230 " distance=2.08 Simple disulfide: pdb=" SG CYS N 232 " - pdb=" SG CYS N 237 " distance=2.07 Simple disulfide: pdb=" SG CYS N 278 " - pdb=" SG CYS N 291 " distance=2.01 Simple disulfide: pdb=" SG CYS N 280 " - pdb=" SG CYS N 289 " distance=2.08 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.06 Simple disulfide: pdb=" SG CYS N 421 " - pdb=" SG CYS N 447 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 417 " distance=2.05 Simple disulfide: pdb=" SG CYS O 124 " - pdb=" SG CYS O 129 " distance=2.07 Simple disulfide: pdb=" SG CYS O 175 " - pdb=" SG CYS O 193 " distance=2.01 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 230 " distance=2.07 Simple disulfide: pdb=" SG CYS O 232 " - pdb=" SG CYS O 237 " distance=2.07 Simple disulfide: pdb=" SG CYS O 278 " - pdb=" SG CYS O 291 " distance=2.01 Simple disulfide: pdb=" SG CYS O 280 " - pdb=" SG CYS O 289 " distance=2.08 Simple disulfide: pdb=" SG CYS O 318 " - pdb=" SG CYS O 337 " distance=2.06 Simple disulfide: pdb=" SG CYS O 421 " - pdb=" SG CYS O 447 " distance=2.09 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS P 92 " - pdb=" SG CYS P 417 " distance=2.05 Simple disulfide: pdb=" SG CYS P 124 " - pdb=" SG CYS P 129 " distance=2.07 Simple disulfide: pdb=" SG CYS P 175 " - pdb=" SG CYS P 193 " distance=2.01 Simple disulfide: pdb=" SG CYS P 183 " - pdb=" SG CYS P 230 " distance=2.07 Simple disulfide: pdb=" SG CYS P 232 " - pdb=" SG CYS P 237 " distance=2.07 Simple disulfide: pdb=" SG CYS P 278 " - pdb=" SG CYS P 291 " distance=2.01 Simple disulfide: pdb=" SG CYS P 280 " - pdb=" SG CYS P 289 " distance=2.08 Simple disulfide: pdb=" SG CYS P 318 " - pdb=" SG CYS P 337 " distance=2.06 Simple disulfide: pdb=" SG CYS P 421 " - pdb=" SG CYS P 447 " distance=2.09 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 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG 1 1 " - " ASN P 86 " " NAG 2 1 " - " ASN P 146 " " NAG 3 1 " - " ASN P 200 " " NAG 4 1 " - " ASN P 234 " " NAG 6 1 " - " ASN P 329 " " NAG 7 1 " - " ASN P 367 " " NAG a 1 " - " ASN M 86 " " NAG b 1 " - " ASN M 146 " " NAG c 1 " - " ASN M 200 " " NAG d 1 " - " ASN M 234 " " NAG f 1 " - " ASN M 329 " " NAG g 1 " - " ASN M 367 " " NAG i 1 " - " ASN N 86 " " NAG j 1 " - " ASN N 146 " " NAG k 1 " - " ASN N 200 " " NAG l 1 " - " ASN N 234 " " NAG n 1 " - " ASN N 329 " " NAG o 1 " - " ASN N 367 " " NAG q 1 " - " ASN O 86 " " NAG r 1 " - " ASN O 146 " " NAG s 1 " - " ASN O 200 " " NAG t 1 " - " ASN O 234 " " NAG v 1 " - " ASN O 329 " " NAG w 1 " - " ASN O 367 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 886.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.828A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.553A pdb=" N ALA M 110 " --> pdb=" O ILE M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.629A pdb=" N SER M 145 " --> pdb=" O ASN M 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN M 146 " --> pdb=" O VAL M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 142 through 146' Processing helix chain 'M' and resid 197 through 200 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER N 145 " --> pdb=" O ASN N 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN N 146 " --> pdb=" O VAL N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 142 through 146' Processing helix chain 'N' and resid 197 through 200 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.787A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 110 removed outlier: 3.551A pdb=" N ALA O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.584A pdb=" N SER O 145 " --> pdb=" O ASN O 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN O 146 " --> pdb=" O VAL O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 146' Processing helix chain 'O' and resid 197 through 200 Processing helix chain 'J' and resid 27 through 31 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA P 110 " --> pdb=" O ILE P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER P 145 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN P 146 " --> pdb=" O VAL P 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 197 through 200 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.414A pdb=" N LEU E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.868A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 33 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 97 through 102 removed outlier: 5.336A pdb=" N CYS M 447 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG M 420 " --> pdb=" O GLY M 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP M 115 " --> pdb=" O THR M 138 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR M 138 " --> pdb=" O TRP M 115 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR M 117 " --> pdb=" O GLN M 136 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN M 136 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU M 119 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU M 134 " --> pdb=" O GLU M 119 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU M 158 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS M 172 " --> pdb=" O MET M 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 179 through 184 removed outlier: 3.537A pdb=" N SER M 179 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR M 207 " --> pdb=" O LEU M 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU M 211 " --> pdb=" O TYR M 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 224 through 225 removed outlier: 3.501A pdb=" N VAL M 231 " --> pdb=" O THR M 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU M 258 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 276 through 283 removed outlier: 5.416A pdb=" N GLU M 277 " --> pdb=" O ARG M 292 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG M 292 " --> pdb=" O GLU M 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 352 through 356 removed outlier: 4.441A pdb=" N TRP M 352 " --> pdb=" O GLY M 363 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 363 " --> pdb=" O TRP M 352 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU M 372 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL M 398 " --> pdb=" O LEU M 372 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR M 374 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL M 396 " --> pdb=" O TYR M 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR M 376 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG M 394 " --> pdb=" O THR M 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.412A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.870A pdb=" N GLN I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 102 removed outlier: 5.347A pdb=" N CYS N 447 " --> pdb=" O PRO N 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG N 420 " --> pdb=" O GLY N 448 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP N 115 " --> pdb=" O THR N 138 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR N 138 " --> pdb=" O TRP N 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR N 117 " --> pdb=" O GLN N 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN N 136 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU N 119 " --> pdb=" O LEU N 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU N 134 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU N 158 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 172 " --> pdb=" O MET N 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 179 through 184 removed outlier: 3.551A pdb=" N SER N 179 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR N 207 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU N 211 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 224 through 225 Processing sheet with id=AC4, first strand: chain 'N' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU N 258 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU N 277 " --> pdb=" O ARG N 292 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG N 292 " --> pdb=" O GLU N 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 352 through 356 removed outlier: 4.442A pdb=" N TRP N 352 " --> pdb=" O GLY N 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY N 363 " --> pdb=" O TRP N 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU N 372 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL N 398 " --> pdb=" O LEU N 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR N 374 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL N 396 " --> pdb=" O TYR N 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR N 376 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 394 " --> pdb=" O THR N 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.411A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.866A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS O 447 " --> pdb=" O PRO O 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG O 420 " --> pdb=" O GLY O 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP O 115 " --> pdb=" O THR O 138 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR O 138 " --> pdb=" O TRP O 115 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR O 117 " --> pdb=" O GLN O 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN O 136 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU O 119 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU O 134 " --> pdb=" O GLU O 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU O 158 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS O 172 " --> pdb=" O MET O 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER O 179 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR O 207 " --> pdb=" O LEU O 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU O 211 " --> pdb=" O TYR O 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 224 through 225 Processing sheet with id=AD7, first strand: chain 'O' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU O 258 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE O 262 " --> pdb=" O GLU O 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 276 through 283 removed outlier: 5.427A pdb=" N GLU O 277 " --> pdb=" O ARG O 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG O 292 " --> pdb=" O GLU O 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 352 through 356 removed outlier: 4.443A pdb=" N TRP O 352 " --> pdb=" O GLY O 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY O 363 " --> pdb=" O TRP O 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU O 372 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL O 398 " --> pdb=" O LEU O 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR O 374 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL O 396 " --> pdb=" O TYR O 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR O 376 " --> pdb=" O ARG O 394 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG O 394 " --> pdb=" O THR O 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.414A pdb=" N LEU J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AE4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.865A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU K 33 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS P 447 " --> pdb=" O PRO P 99 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG P 420 " --> pdb=" O GLY P 448 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP P 115 " --> pdb=" O THR P 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR P 138 " --> pdb=" O TRP P 115 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR P 117 " --> pdb=" O GLN P 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN P 136 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU P 119 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU P 134 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU P 158 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS P 172 " --> pdb=" O MET P 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER P 179 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR P 207 " --> pdb=" O LEU P 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU P 211 " --> pdb=" O TYR P 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 224 through 225 Processing sheet with id=AF1, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU P 258 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE P 262 " --> pdb=" O GLU P 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU P 277 " --> pdb=" O ARG P 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG P 292 " --> pdb=" O GLU P 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 352 through 356 removed outlier: 4.439A pdb=" N TRP P 352 " --> pdb=" O GLY P 363 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY P 363 " --> pdb=" O TRP P 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU P 372 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL P 398 " --> pdb=" O LEU P 372 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR P 374 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL P 396 " --> pdb=" O TYR P 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR P 376 " --> pdb=" O ARG P 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG P 394 " --> pdb=" O THR P 376 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1632 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: 4.42 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3376 1.31 - 1.44: 5850 1.44 - 1.58: 11529 1.58 - 1.71: 0 1.71 - 1.85: 144 Bond restraints: 20899 Sorted by residual: bond pdb=" C PRO N 301 " pdb=" O PRO N 301 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.08e-02 8.57e+03 3.60e+01 bond pdb=" C PRO P 301 " pdb=" O PRO P 301 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.08e-02 8.57e+03 3.60e+01 bond pdb=" C PRO O 301 " pdb=" O PRO O 301 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.08e-02 8.57e+03 3.56e+01 bond pdb=" C PRO M 301 " pdb=" O PRO M 301 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.08e-02 8.57e+03 3.25e+01 bond pdb=" C PRO P 90 " pdb=" O PRO P 90 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.18e-02 7.18e+03 2.74e+01 ... (remaining 20894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.69: 28384 9.69 - 19.38: 1 19.38 - 29.07: 0 29.07 - 38.75: 1 38.75 - 48.44: 2 Bond angle restraints: 28388 Sorted by residual: angle pdb=" OE1 GLN I 70 " pdb=" CD GLN I 70 " pdb=" NE2 GLN I 70 " ideal model delta sigma weight residual 122.60 79.48 43.12 1.00e+00 1.00e+00 1.86e+03 angle pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " pdb=" NE2 GLN I 70 " ideal model delta sigma weight residual 116.40 164.84 -48.44 1.50e+00 4.44e-01 1.04e+03 angle pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " pdb=" OE1 GLN I 70 " ideal model delta sigma weight residual 120.80 86.77 34.03 2.00e+00 2.50e-01 2.90e+02 angle pdb=" CB GLN I 70 " pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " ideal model delta sigma weight residual 112.60 124.86 -12.26 1.70e+00 3.46e-01 5.20e+01 angle pdb=" N ILE M 397 " pdb=" CA ILE M 397 " pdb=" C ILE M 397 " ideal model delta sigma weight residual 111.90 107.13 4.77 8.10e-01 1.52e+00 3.47e+01 ... (remaining 28383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12631 22.12 - 44.25: 563 44.25 - 66.37: 100 66.37 - 88.50: 111 88.50 - 110.62: 61 Dihedral angle restraints: 13466 sinusoidal: 6336 harmonic: 7130 Sorted by residual: dihedral pdb=" CA GLU M 276 " pdb=" C GLU M 276 " pdb=" N GLU M 277 " pdb=" CA GLU M 277 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N TYR E 103 " pdb=" CA TYR E 103 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CB CYS P 318 " pdb=" SG CYS P 318 " pdb=" SG CYS P 337 " pdb=" CB CYS P 337 " ideal model delta sinusoidal sigma weight residual 93.00 137.43 -44.43 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 13463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1650 0.065 - 0.130: 1109 0.130 - 0.195: 461 0.195 - 0.259: 119 0.259 - 0.324: 15 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.67e+01 ... (remaining 3351 not shown) Planarity restraints: 3550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 121 " -0.116 2.00e-02 2.50e+03 6.06e-02 7.34e+01 pdb=" CG TYR N 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR N 121 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR N 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR N 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR N 121 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR N 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 121 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 121 " 0.116 2.00e-02 2.50e+03 6.05e-02 7.32e+01 pdb=" CG TYR O 121 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR O 121 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR O 121 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR O 121 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR O 121 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR O 121 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 121 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 121 " -0.116 2.00e-02 2.50e+03 6.04e-02 7.30e+01 pdb=" CG TYR P 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR P 121 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR P 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR P 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR P 121 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR P 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 121 " -0.081 2.00e-02 2.50e+03 ... (remaining 3547 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1956 2.75 - 3.29: 20789 3.29 - 3.83: 34655 3.83 - 4.36: 47087 4.36 - 4.90: 76572 Nonbonded interactions: 181059 Sorted by model distance: nonbonded pdb=" O GLY N 345 " pdb="CA CA N2000 " model vdw 2.213 2.510 nonbonded pdb=" O GLY P 345 " pdb="CA CA P2000 " model vdw 2.214 2.510 nonbonded pdb=" O GLY O 345 " pdb="CA CA O2000 " model vdw 2.214 2.510 nonbonded pdb=" O HIS M 347 " pdb="CA CA M 501 " model vdw 2.236 2.510 nonbonded pdb=" O HIS O 347 " pdb="CA CA O2000 " model vdw 2.237 2.510 ... (remaining 181054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain 'a' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '6' selection = chain '7' selection = chain 'f' selection = chain 'g' selection = chain 'n' selection = chain 'o' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 82 through 501) selection = (chain 'N' and (resid 82 through 244 or resid 250 through 2000)) selection = (chain 'O' and (resid 82 through 244 or resid 250 through 2000)) selection = (chain 'P' and (resid 82 through 244 or resid 250 through 2000)) } ncs_group { reference = chain 'b' selection = chain 'r' } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.610 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.016 0.075 21029 Z= 1.083 Angle : 1.910 48.443 28734 Z= 1.226 Chirality : 0.095 0.324 3354 Planarity : 0.012 0.073 3526 Dihedral : 16.960 110.622 8790 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.22 % Favored : 93.46 % Rotamer: Outliers : 0.56 % Allowed : 2.91 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.15), residues: 2477 helix: -3.10 (0.72), residues: 28 sheet: -0.77 (0.16), residues: 918 loop : -1.56 (0.14), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG M 224 TYR 0.116 0.016 TYR N 121 PHE 0.087 0.013 PHE O 205 TRP 0.081 0.016 TRP M 458 HIS 0.024 0.005 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.01577 (20899) covalent geometry : angle 1.86663 (28388) SS BOND : bond 0.03542 ( 44) SS BOND : angle 2.31605 ( 88) hydrogen bonds : bond 0.14365 ( 643) hydrogen bonds : angle 8.61819 ( 1632) link_ALPHA1-2 : bond 0.00193 ( 4) link_ALPHA1-2 : angle 4.58169 ( 12) link_ALPHA1-3 : bond 0.02071 ( 8) link_ALPHA1-3 : angle 3.04705 ( 24) link_ALPHA1-6 : bond 0.01246 ( 10) link_ALPHA1-6 : angle 3.01511 ( 30) link_BETA1-4 : bond 0.01271 ( 40) link_BETA1-4 : angle 4.34875 ( 120) link_NAG-ASN : bond 0.02409 ( 24) link_NAG-ASN : angle 5.86405 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 448 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 ARG cc_start: 0.9517 (mmm160) cc_final: 0.9290 (mmt-90) REVERT: E 31 LYS cc_start: 0.9238 (tttp) cc_final: 0.9018 (tttm) REVERT: E 65 GLN cc_start: 0.8945 (tt0) cc_final: 0.8511 (mt0) REVERT: E 81 MET cc_start: 0.9609 (ttp) cc_final: 0.8887 (tmm) REVERT: E 82 GLU cc_start: 0.9173 (tt0) cc_final: 0.8733 (tm-30) REVERT: F 4 MET cc_start: 0.9184 (mmm) cc_final: 0.8966 (tpp) REVERT: F 24 ARG cc_start: 0.9468 (mpt-90) cc_final: 0.9213 (mtp-110) REVERT: F 42 GLN cc_start: 0.8532 (mt0) cc_final: 0.8214 (mp10) REVERT: F 54 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8355 (mtm-85) REVERT: F 89 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8930 (tt0) REVERT: M 119 GLU cc_start: 0.9523 (mp0) cc_final: 0.9158 (mp0) REVERT: G 65 GLN cc_start: 0.8760 (tt0) cc_final: 0.8404 (mt0) REVERT: G 81 MET cc_start: 0.9609 (ttp) cc_final: 0.8850 (tmm) REVERT: G 82 GLU cc_start: 0.9156 (tt0) cc_final: 0.8762 (tm-30) REVERT: I 4 MET cc_start: 0.9197 (mmm) cc_final: 0.8983 (tpp) REVERT: I 11 LEU cc_start: 0.9263 (tp) cc_final: 0.8974 (tt) REVERT: I 24 ARG cc_start: 0.9455 (mpt-90) cc_final: 0.9211 (mtp-110) REVERT: I 42 GLN cc_start: 0.8532 (mt0) cc_final: 0.8219 (mp10) REVERT: I 54 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8422 (mtm-85) REVERT: I 89 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8899 (tt0) REVERT: N 119 GLU cc_start: 0.9532 (mp0) cc_final: 0.9168 (mp0) REVERT: H 65 GLN cc_start: 0.8759 (tt0) cc_final: 0.8404 (mt0) REVERT: H 81 MET cc_start: 0.9609 (ttp) cc_final: 0.8851 (tmm) REVERT: H 82 GLU cc_start: 0.9155 (tt0) cc_final: 0.8759 (tm-30) REVERT: L 4 MET cc_start: 0.9198 (mmm) cc_final: 0.8981 (tpp) REVERT: L 11 LEU cc_start: 0.9271 (tp) cc_final: 0.8979 (tt) REVERT: L 24 ARG cc_start: 0.9476 (mpt-90) cc_final: 0.9187 (mtp-110) REVERT: L 42 GLN cc_start: 0.8529 (mt0) cc_final: 0.8217 (mp10) REVERT: L 54 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: L 89 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8931 (tt0) REVERT: O 119 GLU cc_start: 0.9532 (mp0) cc_final: 0.9166 (mp0) REVERT: J 13 ARG cc_start: 0.9499 (mmm160) cc_final: 0.9298 (mmt-90) REVERT: J 65 GLN cc_start: 0.8760 (tt0) cc_final: 0.8404 (mt0) REVERT: J 81 MET cc_start: 0.9607 (ttp) cc_final: 0.8845 (tmm) REVERT: J 82 GLU cc_start: 0.9153 (tt0) cc_final: 0.8759 (tm-30) REVERT: K 4 MET cc_start: 0.9192 (mmm) cc_final: 0.8973 (tpp) REVERT: K 11 LEU cc_start: 0.9266 (tp) cc_final: 0.8978 (tt) REVERT: K 24 ARG cc_start: 0.9476 (mpt-90) cc_final: 0.9202 (mtp-110) REVERT: K 42 GLN cc_start: 0.8530 (mt0) cc_final: 0.8218 (mp10) REVERT: K 54 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8446 (mtm-85) REVERT: K 89 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8892 (tt0) REVERT: P 106 ILE cc_start: 0.9462 (mt) cc_final: 0.9231 (mp) REVERT: P 119 GLU cc_start: 0.9531 (mp0) cc_final: 0.9164 (mp0) outliers start: 12 outliers final: 8 residues processed: 456 average time/residue: 0.1932 time to fit residues: 127.8330 Evaluate side-chains 353 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain M residue 178 TRP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain N residue 178 TRP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain O residue 178 TRP Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain P residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN M 147 ASN M 391 GLN G 62 GLN N 147 ASN H 62 GLN O 147 ASN O 391 GLN J 62 GLN P 147 ASN P 391 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052018 restraints weight = 60435.136| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.80 r_work: 0.2657 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21029 Z= 0.176 Angle : 0.789 7.137 28734 Z= 0.397 Chirality : 0.049 0.181 3354 Planarity : 0.004 0.036 3526 Dihedral : 12.761 76.594 4472 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 1.03 % Allowed : 9.82 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2477 helix: -2.27 (0.77), residues: 28 sheet: -0.10 (0.18), residues: 886 loop : -0.73 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 106 TYR 0.017 0.002 TYR O 121 PHE 0.018 0.002 PHE L 83 TRP 0.020 0.002 TRP O 115 HIS 0.002 0.001 HIS N 347 Details of bonding type rmsd covalent geometry : bond 0.00379 (20899) covalent geometry : angle 0.75553 (28388) SS BOND : bond 0.00427 ( 44) SS BOND : angle 0.74328 ( 88) hydrogen bonds : bond 0.04485 ( 643) hydrogen bonds : angle 7.38775 ( 1632) link_ALPHA1-2 : bond 0.00808 ( 4) link_ALPHA1-2 : angle 1.90173 ( 12) link_ALPHA1-3 : bond 0.01194 ( 8) link_ALPHA1-3 : angle 2.19008 ( 24) link_ALPHA1-6 : bond 0.00787 ( 10) link_ALPHA1-6 : angle 1.22395 ( 30) link_BETA1-4 : bond 0.00454 ( 40) link_BETA1-4 : angle 2.75567 ( 120) link_NAG-ASN : bond 0.00289 ( 24) link_NAG-ASN : angle 2.71575 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 385 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8191 (mm-40) REVERT: E 23 LYS cc_start: 0.9230 (tptm) cc_final: 0.9007 (tptp) REVERT: E 31 LYS cc_start: 0.8684 (tttp) cc_final: 0.8275 (tttm) REVERT: E 65 GLN cc_start: 0.8204 (tt0) cc_final: 0.7745 (mt0) REVERT: E 81 MET cc_start: 0.9382 (ttp) cc_final: 0.8522 (tmm) REVERT: E 82 GLU cc_start: 0.8532 (tt0) cc_final: 0.7935 (tm-30) REVERT: E 89 GLU cc_start: 0.9561 (mp0) cc_final: 0.9275 (pm20) REVERT: F 11 LEU cc_start: 0.9123 (tp) cc_final: 0.8645 (tp) REVERT: F 42 GLN cc_start: 0.7987 (mt0) cc_final: 0.7733 (mp10) REVERT: F 48 ILE cc_start: 0.8956 (mm) cc_final: 0.8745 (mm) REVERT: F 70 GLN cc_start: 0.8743 (mm110) cc_final: 0.8384 (mm110) REVERT: F 79 GLN cc_start: 0.9184 (mm110) cc_final: 0.8843 (mp10) REVERT: F 104 LYS cc_start: 0.8620 (tppt) cc_final: 0.7946 (tptp) REVERT: M 113 ASP cc_start: 0.8787 (p0) cc_final: 0.8434 (p0) REVERT: M 119 GLU cc_start: 0.9030 (mp0) cc_final: 0.8456 (mp0) REVERT: M 227 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7418 (mp0) REVERT: G 3 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8193 (mm-40) REVERT: G 23 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9051 (tptp) REVERT: G 63 LYS cc_start: 0.9534 (mtpp) cc_final: 0.9279 (mtmm) REVERT: G 65 GLN cc_start: 0.7872 (tt0) cc_final: 0.7579 (mt0) REVERT: G 81 MET cc_start: 0.9366 (ttp) cc_final: 0.8531 (tmm) REVERT: G 82 GLU cc_start: 0.8544 (tt0) cc_final: 0.7967 (tm-30) REVERT: I 42 GLN cc_start: 0.8048 (mt0) cc_final: 0.7777 (mp10) REVERT: I 70 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8219 (mm-40) REVERT: I 79 GLN cc_start: 0.9205 (mm110) cc_final: 0.8776 (mm110) REVERT: I 89 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9133 (tt0) REVERT: N 113 ASP cc_start: 0.8731 (p0) cc_final: 0.8369 (p0) REVERT: N 119 GLU cc_start: 0.9097 (mp0) cc_final: 0.8573 (mp0) REVERT: H 3 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8191 (mm-40) REVERT: H 23 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9045 (tptp) REVERT: H 65 GLN cc_start: 0.7859 (tt0) cc_final: 0.7598 (mt0) REVERT: H 81 MET cc_start: 0.9354 (ttp) cc_final: 0.8504 (tmm) REVERT: H 82 GLU cc_start: 0.8541 (tt0) cc_final: 0.7963 (tm-30) REVERT: L 42 GLN cc_start: 0.8067 (mt0) cc_final: 0.7790 (mp10) REVERT: L 70 GLN cc_start: 0.8775 (mm110) cc_final: 0.8492 (mm110) REVERT: L 79 GLN cc_start: 0.9189 (mm110) cc_final: 0.8749 (mm110) REVERT: O 113 ASP cc_start: 0.8737 (p0) cc_final: 0.8375 (p0) REVERT: O 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8515 (mp0) REVERT: J 3 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8197 (mm-40) REVERT: J 13 ARG cc_start: 0.9210 (mmm160) cc_final: 0.8564 (mmt180) REVERT: J 23 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9055 (tptp) REVERT: J 63 LYS cc_start: 0.9527 (mtpp) cc_final: 0.9276 (mtmm) REVERT: J 65 GLN cc_start: 0.7873 (tt0) cc_final: 0.7574 (mt0) REVERT: J 81 MET cc_start: 0.9362 (ttp) cc_final: 0.8522 (tmm) REVERT: J 82 GLU cc_start: 0.8548 (tt0) cc_final: 0.7973 (tm-30) REVERT: K 42 GLN cc_start: 0.8056 (mt0) cc_final: 0.7783 (mp10) REVERT: K 70 GLN cc_start: 0.8690 (mm110) cc_final: 0.8368 (mm110) REVERT: K 79 GLN cc_start: 0.9212 (mm110) cc_final: 0.8781 (mm110) REVERT: K 89 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9123 (tt0) REVERT: P 113 ASP cc_start: 0.8751 (p0) cc_final: 0.8394 (p0) REVERT: P 119 GLU cc_start: 0.9081 (mp0) cc_final: 0.8566 (mp0) outliers start: 22 outliers final: 11 residues processed: 394 average time/residue: 0.1467 time to fit residues: 85.0121 Evaluate side-chains 353 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 338 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain P residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051886 restraints weight = 60992.352| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.88 r_work: 0.2663 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21029 Z= 0.164 Angle : 0.720 8.493 28734 Z= 0.353 Chirality : 0.046 0.161 3354 Planarity : 0.004 0.048 3526 Dihedral : 9.845 60.747 4456 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 11.13 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2477 helix: -1.79 (0.86), residues: 28 sheet: -0.20 (0.17), residues: 922 loop : -0.37 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.019 0.002 TYR M 121 PHE 0.018 0.002 PHE L 83 TRP 0.017 0.002 TRP N 115 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00358 (20899) covalent geometry : angle 0.69109 (28388) SS BOND : bond 0.00304 ( 44) SS BOND : angle 0.48374 ( 88) hydrogen bonds : bond 0.03866 ( 643) hydrogen bonds : angle 6.79641 ( 1632) link_ALPHA1-2 : bond 0.00661 ( 4) link_ALPHA1-2 : angle 2.13099 ( 12) link_ALPHA1-3 : bond 0.00882 ( 8) link_ALPHA1-3 : angle 1.90040 ( 24) link_ALPHA1-6 : bond 0.00618 ( 10) link_ALPHA1-6 : angle 1.42994 ( 30) link_BETA1-4 : bond 0.00510 ( 40) link_BETA1-4 : angle 2.47916 ( 120) link_NAG-ASN : bond 0.00190 ( 24) link_NAG-ASN : angle 2.26216 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 354 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8194 (mm-30) REVERT: E 23 LYS cc_start: 0.9208 (tptm) cc_final: 0.8950 (tptm) REVERT: E 65 GLN cc_start: 0.8405 (tt0) cc_final: 0.7945 (mt0) REVERT: E 81 MET cc_start: 0.9358 (ttp) cc_final: 0.8645 (tmm) REVERT: E 82 GLU cc_start: 0.8567 (tt0) cc_final: 0.7933 (tm-30) REVERT: F 4 MET cc_start: 0.9040 (tpp) cc_final: 0.8599 (tpp) REVERT: F 42 GLN cc_start: 0.8103 (mt0) cc_final: 0.7803 (mp10) REVERT: F 70 GLN cc_start: 0.8659 (mm110) cc_final: 0.8338 (mm110) REVERT: F 101 GLN cc_start: 0.7812 (pm20) cc_final: 0.7585 (pm20) REVERT: M 113 ASP cc_start: 0.8785 (p0) cc_final: 0.8322 (p0) REVERT: M 119 GLU cc_start: 0.9027 (mp0) cc_final: 0.8484 (mp0) REVERT: M 241 MET cc_start: 0.9397 (mtp) cc_final: 0.8977 (mtm) REVERT: G 10 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8112 (mm-30) REVERT: G 23 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: G 65 GLN cc_start: 0.8093 (tt0) cc_final: 0.7779 (mt0) REVERT: G 81 MET cc_start: 0.9350 (ttp) cc_final: 0.8989 (tmm) REVERT: G 82 GLU cc_start: 0.8566 (tt0) cc_final: 0.7893 (tm-30) REVERT: I 42 GLN cc_start: 0.8107 (mt0) cc_final: 0.7837 (mp10) REVERT: I 70 GLN cc_start: 0.8716 (mt0) cc_final: 0.8323 (mm-40) REVERT: I 101 GLN cc_start: 0.7811 (pm20) cc_final: 0.7584 (pm20) REVERT: I 104 LYS cc_start: 0.8809 (tptt) cc_final: 0.8574 (tptt) REVERT: N 113 ASP cc_start: 0.8744 (p0) cc_final: 0.8263 (p0) REVERT: N 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8536 (mp0) REVERT: N 241 MET cc_start: 0.9400 (mtp) cc_final: 0.8956 (mtm) REVERT: N 362 MET cc_start: 0.8115 (ptp) cc_final: 0.7713 (ptm) REVERT: H 10 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8116 (mm-30) REVERT: H 23 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8892 (tptp) REVERT: H 46 GLU cc_start: 0.8444 (tt0) cc_final: 0.8116 (tt0) REVERT: H 65 GLN cc_start: 0.8023 (tt0) cc_final: 0.7730 (mt0) REVERT: H 81 MET cc_start: 0.9300 (ttp) cc_final: 0.8961 (tmm) REVERT: H 82 GLU cc_start: 0.8557 (tt0) cc_final: 0.7887 (tm-30) REVERT: L 4 MET cc_start: 0.9030 (tpp) cc_final: 0.8615 (tpp) REVERT: L 42 GLN cc_start: 0.8133 (mt0) cc_final: 0.7855 (mp10) REVERT: L 70 GLN cc_start: 0.8728 (mm110) cc_final: 0.8357 (mm110) REVERT: L 101 GLN cc_start: 0.7844 (pm20) cc_final: 0.7623 (pm20) REVERT: O 113 ASP cc_start: 0.8746 (p0) cc_final: 0.8245 (p0) REVERT: O 119 GLU cc_start: 0.9064 (mp0) cc_final: 0.8530 (mp0) REVERT: O 241 MET cc_start: 0.9396 (mtp) cc_final: 0.8942 (mtm) REVERT: O 362 MET cc_start: 0.8125 (ptp) cc_final: 0.7712 (ptm) REVERT: J 10 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8091 (mm-30) REVERT: J 23 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8908 (tptp) REVERT: J 65 GLN cc_start: 0.8078 (tt0) cc_final: 0.7767 (mt0) REVERT: J 81 MET cc_start: 0.9308 (ttp) cc_final: 0.8973 (tmm) REVERT: J 82 GLU cc_start: 0.8564 (tt0) cc_final: 0.7892 (tm-30) REVERT: K 42 GLN cc_start: 0.8130 (mt0) cc_final: 0.7854 (mp10) REVERT: K 70 GLN cc_start: 0.8703 (mm110) cc_final: 0.8394 (mm110) REVERT: K 101 GLN cc_start: 0.7825 (pm20) cc_final: 0.7594 (pm20) REVERT: K 104 LYS cc_start: 0.8826 (tptt) cc_final: 0.8589 (tptt) REVERT: P 113 ASP cc_start: 0.8757 (p0) cc_final: 0.7897 (p0) REVERT: P 119 GLU cc_start: 0.9060 (mp0) cc_final: 0.8492 (mp0) REVERT: P 241 MET cc_start: 0.9398 (mtp) cc_final: 0.8949 (mtm) REVERT: P 362 MET cc_start: 0.8110 (ptp) cc_final: 0.7702 (ptm) outliers start: 36 outliers final: 32 residues processed: 367 average time/residue: 0.1403 time to fit residues: 77.6613 Evaluate side-chains 369 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 219 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 391 GLN P 391 GLN ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049564 restraints weight = 60135.765| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.79 r_work: 0.2674 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21029 Z= 0.184 Angle : 0.683 8.035 28734 Z= 0.336 Chirality : 0.045 0.192 3354 Planarity : 0.004 0.068 3526 Dihedral : 7.551 51.264 4456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 2.02 % Allowed : 12.35 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2477 helix: -1.61 (0.89), residues: 28 sheet: -0.23 (0.17), residues: 917 loop : -0.20 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 87 TYR 0.014 0.002 TYR H 80 PHE 0.016 0.002 PHE F 83 TRP 0.015 0.002 TRP M 178 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00409 (20899) covalent geometry : angle 0.65669 (28388) SS BOND : bond 0.00300 ( 44) SS BOND : angle 0.44929 ( 88) hydrogen bonds : bond 0.03632 ( 643) hydrogen bonds : angle 6.53032 ( 1632) link_ALPHA1-2 : bond 0.00572 ( 4) link_ALPHA1-2 : angle 2.13042 ( 12) link_ALPHA1-3 : bond 0.00829 ( 8) link_ALPHA1-3 : angle 2.05998 ( 24) link_ALPHA1-6 : bond 0.00511 ( 10) link_ALPHA1-6 : angle 1.46508 ( 30) link_BETA1-4 : bond 0.00411 ( 40) link_BETA1-4 : angle 2.26412 ( 120) link_NAG-ASN : bond 0.00274 ( 24) link_NAG-ASN : angle 2.10763 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 355 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8438 (mm-30) REVERT: E 23 LYS cc_start: 0.9286 (tptm) cc_final: 0.9016 (tptm) REVERT: E 46 GLU cc_start: 0.8633 (tt0) cc_final: 0.8407 (tt0) REVERT: E 65 GLN cc_start: 0.8552 (tt0) cc_final: 0.8067 (mt0) REVERT: E 81 MET cc_start: 0.9371 (ttp) cc_final: 0.9124 (tmm) REVERT: E 82 GLU cc_start: 0.8710 (tt0) cc_final: 0.8031 (tm-30) REVERT: F 42 GLN cc_start: 0.8385 (mt0) cc_final: 0.7996 (mp10) REVERT: F 70 GLN cc_start: 0.8755 (mm110) cc_final: 0.8354 (mm110) REVERT: F 101 GLN cc_start: 0.8062 (pm20) cc_final: 0.7770 (pm20) REVERT: F 104 LYS cc_start: 0.9001 (tptt) cc_final: 0.8760 (tptt) REVERT: M 113 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8047 (p0) REVERT: M 119 GLU cc_start: 0.9048 (mp0) cc_final: 0.8324 (mp0) REVERT: M 362 MET cc_start: 0.8326 (ptp) cc_final: 0.7936 (ptm) REVERT: G 10 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8438 (mm-30) REVERT: G 23 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8994 (tptp) REVERT: G 46 GLU cc_start: 0.8629 (tt0) cc_final: 0.8422 (tt0) REVERT: G 65 GLN cc_start: 0.8216 (tt0) cc_final: 0.7883 (mt0) REVERT: G 81 MET cc_start: 0.9347 (ttp) cc_final: 0.9121 (tmm) REVERT: G 82 GLU cc_start: 0.8692 (tt0) cc_final: 0.7970 (tm-30) REVERT: G 89 GLU cc_start: 0.9327 (pm20) cc_final: 0.9095 (pm20) REVERT: I 42 GLN cc_start: 0.8345 (mt0) cc_final: 0.7964 (mp10) REVERT: I 70 GLN cc_start: 0.8855 (mt0) cc_final: 0.8431 (mm110) REVERT: I 101 GLN cc_start: 0.8091 (pm20) cc_final: 0.7800 (pm20) REVERT: N 113 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8045 (p0) REVERT: N 119 GLU cc_start: 0.9042 (mp0) cc_final: 0.8324 (mp0) REVERT: N 362 MET cc_start: 0.8308 (ptp) cc_final: 0.7937 (ptm) REVERT: H 10 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8446 (mm-30) REVERT: H 23 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8989 (tptp) REVERT: H 46 GLU cc_start: 0.8688 (tt0) cc_final: 0.8427 (tt0) REVERT: H 65 GLN cc_start: 0.8315 (tt0) cc_final: 0.8029 (mt0) REVERT: H 81 MET cc_start: 0.9345 (ttp) cc_final: 0.9106 (tmm) REVERT: H 82 GLU cc_start: 0.8683 (tt0) cc_final: 0.7980 (tm-30) REVERT: H 89 GLU cc_start: 0.9325 (pm20) cc_final: 0.9090 (pm20) REVERT: L 42 GLN cc_start: 0.8360 (mt0) cc_final: 0.8001 (mp10) REVERT: L 70 GLN cc_start: 0.8789 (mm110) cc_final: 0.8436 (mm110) REVERT: L 101 GLN cc_start: 0.8072 (pm20) cc_final: 0.7791 (pm20) REVERT: O 113 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8063 (p0) REVERT: O 119 GLU cc_start: 0.9041 (mp0) cc_final: 0.8323 (mp0) REVERT: O 362 MET cc_start: 0.8323 (ptp) cc_final: 0.7960 (ptm) REVERT: J 10 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8382 (mm-30) REVERT: J 23 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9010 (tptp) REVERT: J 65 GLN cc_start: 0.8206 (tt0) cc_final: 0.7875 (mt0) REVERT: J 81 MET cc_start: 0.9350 (ttp) cc_final: 0.9111 (tmm) REVERT: J 82 GLU cc_start: 0.8681 (tt0) cc_final: 0.7960 (tm-30) REVERT: J 89 GLU cc_start: 0.9323 (pm20) cc_final: 0.9091 (pm20) REVERT: K 42 GLN cc_start: 0.8348 (mt0) cc_final: 0.7987 (mp10) REVERT: K 70 GLN cc_start: 0.8824 (mm110) cc_final: 0.8458 (mm110) REVERT: K 101 GLN cc_start: 0.8058 (pm20) cc_final: 0.7763 (pm20) REVERT: P 113 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8044 (p0) REVERT: P 119 GLU cc_start: 0.9038 (mp0) cc_final: 0.8327 (mp0) REVERT: P 362 MET cc_start: 0.8324 (ptp) cc_final: 0.7966 (ptm) outliers start: 43 outliers final: 33 residues processed: 372 average time/residue: 0.1322 time to fit residues: 74.0537 Evaluate side-chains 380 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 340 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN M 347 HIS M 391 GLN N 347 HIS O 347 HIS P 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.048532 restraints weight = 61461.060| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.80 r_work: 0.2609 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 21029 Z= 0.345 Angle : 0.762 9.721 28734 Z= 0.375 Chirality : 0.047 0.199 3354 Planarity : 0.004 0.037 3526 Dihedral : 7.425 51.394 4456 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.76 % Favored : 95.07 % Rotamer: Outliers : 2.54 % Allowed : 12.07 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.17), residues: 2477 helix: -1.07 (0.97), residues: 28 sheet: -0.38 (0.17), residues: 949 loop : -0.37 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 87 TYR 0.018 0.002 TYR G 80 PHE 0.016 0.002 PHE P 132 TRP 0.012 0.002 TRP E 36 HIS 0.005 0.001 HIS P 168 Details of bonding type rmsd covalent geometry : bond 0.00765 (20899) covalent geometry : angle 0.73281 (28388) SS BOND : bond 0.00418 ( 44) SS BOND : angle 0.53674 ( 88) hydrogen bonds : bond 0.03967 ( 643) hydrogen bonds : angle 6.65860 ( 1632) link_ALPHA1-2 : bond 0.00128 ( 4) link_ALPHA1-2 : angle 2.22205 ( 12) link_ALPHA1-3 : bond 0.00486 ( 8) link_ALPHA1-3 : angle 2.75859 ( 24) link_ALPHA1-6 : bond 0.00218 ( 10) link_ALPHA1-6 : angle 1.68340 ( 30) link_BETA1-4 : bond 0.00334 ( 40) link_BETA1-4 : angle 2.20975 ( 120) link_NAG-ASN : bond 0.00712 ( 24) link_NAG-ASN : angle 2.59647 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8423 (mm-30) REVERT: E 23 LYS cc_start: 0.9303 (tptm) cc_final: 0.8977 (tptp) REVERT: E 65 GLN cc_start: 0.8701 (tt0) cc_final: 0.8166 (mt0) REVERT: E 81 MET cc_start: 0.9449 (ttp) cc_final: 0.9101 (tmm) REVERT: E 82 GLU cc_start: 0.8788 (tt0) cc_final: 0.8074 (tm-30) REVERT: F 4 MET cc_start: 0.9096 (tpp) cc_final: 0.8656 (tpp) REVERT: F 42 GLN cc_start: 0.8539 (mt0) cc_final: 0.8031 (mp10) REVERT: F 70 GLN cc_start: 0.8772 (mm110) cc_final: 0.8441 (mm110) REVERT: F 101 GLN cc_start: 0.8136 (pm20) cc_final: 0.7818 (pm20) REVERT: F 104 LYS cc_start: 0.8992 (tptt) cc_final: 0.8174 (tptt) REVERT: M 113 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8100 (p0) REVERT: M 119 GLU cc_start: 0.9089 (mp0) cc_final: 0.8456 (mp0) REVERT: M 362 MET cc_start: 0.8378 (ptp) cc_final: 0.8038 (ptm) REVERT: G 10 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8559 (mm-30) REVERT: G 23 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8989 (tptp) REVERT: G 65 GLN cc_start: 0.8378 (tt0) cc_final: 0.8054 (mt0) REVERT: G 81 MET cc_start: 0.9418 (ttp) cc_final: 0.9077 (tmm) REVERT: G 82 GLU cc_start: 0.8773 (tt0) cc_final: 0.8044 (tm-30) REVERT: I 4 MET cc_start: 0.9126 (tpp) cc_final: 0.8653 (tpp) REVERT: I 42 GLN cc_start: 0.8527 (mt0) cc_final: 0.8085 (mp10) REVERT: I 70 GLN cc_start: 0.8885 (mt0) cc_final: 0.8506 (mm110) REVERT: I 101 GLN cc_start: 0.8173 (pm20) cc_final: 0.7844 (pm20) REVERT: N 113 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8111 (p0) REVERT: N 119 GLU cc_start: 0.9098 (mp0) cc_final: 0.8447 (mp0) REVERT: N 362 MET cc_start: 0.8365 (ptp) cc_final: 0.8048 (ptm) REVERT: H 10 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8564 (mm-30) REVERT: H 23 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9007 (tptp) REVERT: H 46 GLU cc_start: 0.8708 (tt0) cc_final: 0.8364 (tt0) REVERT: H 65 GLN cc_start: 0.8398 (tt0) cc_final: 0.8059 (mt0) REVERT: H 81 MET cc_start: 0.9402 (ttp) cc_final: 0.9062 (tmm) REVERT: H 82 GLU cc_start: 0.8757 (tt0) cc_final: 0.8020 (tm-30) REVERT: L 4 MET cc_start: 0.9101 (tpp) cc_final: 0.8654 (tpp) REVERT: L 42 GLN cc_start: 0.8533 (mt0) cc_final: 0.8091 (mp10) REVERT: L 70 GLN cc_start: 0.8858 (mm110) cc_final: 0.8535 (mm110) REVERT: L 101 GLN cc_start: 0.8181 (pm20) cc_final: 0.7869 (pm20) REVERT: O 113 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8100 (p0) REVERT: O 119 GLU cc_start: 0.9090 (mp0) cc_final: 0.8445 (mp0) REVERT: O 362 MET cc_start: 0.8378 (ptp) cc_final: 0.8047 (ptm) REVERT: J 10 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8519 (mm-30) REVERT: J 23 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8996 (tptp) REVERT: J 63 LYS cc_start: 0.9606 (mtpp) cc_final: 0.9402 (ptpp) REVERT: J 65 GLN cc_start: 0.8382 (tt0) cc_final: 0.8043 (mt0) REVERT: J 81 MET cc_start: 0.9412 (ttp) cc_final: 0.9076 (tmm) REVERT: J 82 GLU cc_start: 0.8763 (tt0) cc_final: 0.8025 (tm-30) REVERT: K 4 MET cc_start: 0.9131 (tpp) cc_final: 0.8670 (tpp) REVERT: K 42 GLN cc_start: 0.8536 (mt0) cc_final: 0.8092 (mp10) REVERT: K 70 GLN cc_start: 0.8890 (mm110) cc_final: 0.8612 (mm110) REVERT: K 101 GLN cc_start: 0.8180 (pm20) cc_final: 0.7879 (pm20) REVERT: P 113 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8108 (p0) REVERT: P 119 GLU cc_start: 0.9090 (mp0) cc_final: 0.8442 (mp0) REVERT: P 362 MET cc_start: 0.8379 (ptp) cc_final: 0.8040 (ptm) outliers start: 54 outliers final: 38 residues processed: 366 average time/residue: 0.1280 time to fit residues: 71.4566 Evaluate side-chains 370 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 GLN H 65 GLN J 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049511 restraints weight = 59663.434| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.79 r_work: 0.2679 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21029 Z= 0.148 Angle : 0.653 8.093 28734 Z= 0.326 Chirality : 0.044 0.205 3354 Planarity : 0.004 0.046 3526 Dihedral : 6.811 44.948 4456 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 2.11 % Allowed : 13.15 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.17), residues: 2477 helix: -1.37 (0.86), residues: 28 sheet: -0.36 (0.17), residues: 933 loop : -0.12 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.020 0.001 TYR J 80 PHE 0.015 0.001 PHE K 83 TRP 0.017 0.002 TRP M 178 HIS 0.003 0.001 HIS P 274 Details of bonding type rmsd covalent geometry : bond 0.00329 (20899) covalent geometry : angle 0.63438 (28388) SS BOND : bond 0.00239 ( 44) SS BOND : angle 0.42796 ( 88) hydrogen bonds : bond 0.03463 ( 643) hydrogen bonds : angle 6.42989 ( 1632) link_ALPHA1-2 : bond 0.00653 ( 4) link_ALPHA1-2 : angle 2.37339 ( 12) link_ALPHA1-3 : bond 0.00936 ( 8) link_ALPHA1-3 : angle 1.78951 ( 24) link_ALPHA1-6 : bond 0.00565 ( 10) link_ALPHA1-6 : angle 1.39911 ( 30) link_BETA1-4 : bond 0.00419 ( 40) link_BETA1-4 : angle 1.69945 ( 120) link_NAG-ASN : bond 0.00178 ( 24) link_NAG-ASN : angle 1.95395 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 345 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8526 (mm-30) REVERT: E 23 LYS cc_start: 0.9298 (tptm) cc_final: 0.9031 (tptp) REVERT: E 65 GLN cc_start: 0.8700 (tt0) cc_final: 0.8166 (mt0) REVERT: E 81 MET cc_start: 0.9350 (ttp) cc_final: 0.9077 (tmm) REVERT: E 82 GLU cc_start: 0.8773 (tt0) cc_final: 0.8033 (tm-30) REVERT: E 89 GLU cc_start: 0.9419 (pm20) cc_final: 0.9095 (pm20) REVERT: F 42 GLN cc_start: 0.8502 (mt0) cc_final: 0.7996 (mp10) REVERT: F 70 GLN cc_start: 0.8838 (mm110) cc_final: 0.8556 (mm110) REVERT: F 101 GLN cc_start: 0.8125 (pm20) cc_final: 0.7813 (pm20) REVERT: M 113 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8155 (p0) REVERT: M 362 MET cc_start: 0.8234 (ptp) cc_final: 0.7895 (ptm) REVERT: G 10 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8588 (mm-30) REVERT: G 23 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9011 (tptp) REVERT: G 46 GLU cc_start: 0.8544 (tt0) cc_final: 0.8314 (tt0) REVERT: G 65 GLN cc_start: 0.8307 (tt0) cc_final: 0.8054 (mt0) REVERT: G 81 MET cc_start: 0.9336 (ttp) cc_final: 0.8900 (tmm) REVERT: G 82 GLU cc_start: 0.8754 (tt0) cc_final: 0.8116 (tm-30) REVERT: I 42 GLN cc_start: 0.8449 (mt0) cc_final: 0.8058 (mp10) REVERT: I 70 GLN cc_start: 0.8917 (mt0) cc_final: 0.8621 (mm110) REVERT: I 101 GLN cc_start: 0.8142 (pm20) cc_final: 0.7831 (pm20) REVERT: I 104 LYS cc_start: 0.8957 (tptp) cc_final: 0.8167 (tptp) REVERT: N 113 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8195 (p0) REVERT: N 362 MET cc_start: 0.8204 (ptp) cc_final: 0.7859 (ptm) REVERT: H 10 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8581 (mm-30) REVERT: H 23 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9019 (tptp) REVERT: H 46 GLU cc_start: 0.8713 (tt0) cc_final: 0.8360 (tt0) REVERT: H 65 GLN cc_start: 0.8329 (tt0) cc_final: 0.8086 (mt0) REVERT: H 81 MET cc_start: 0.9326 (ttp) cc_final: 0.8950 (tmm) REVERT: H 82 GLU cc_start: 0.8732 (tt0) cc_final: 0.8135 (tm-30) REVERT: L 42 GLN cc_start: 0.8466 (mt0) cc_final: 0.8075 (mp10) REVERT: L 70 GLN cc_start: 0.8885 (mm110) cc_final: 0.8622 (mm110) REVERT: L 101 GLN cc_start: 0.8142 (pm20) cc_final: 0.7865 (pm20) REVERT: O 113 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8168 (p0) REVERT: O 362 MET cc_start: 0.8224 (ptp) cc_final: 0.7887 (ptm) REVERT: J 10 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8551 (mm-30) REVERT: J 23 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9019 (tptp) REVERT: J 65 GLN cc_start: 0.8298 (tt0) cc_final: 0.8043 (mt0) REVERT: J 81 MET cc_start: 0.9330 (ttp) cc_final: 0.8895 (tmm) REVERT: J 82 GLU cc_start: 0.8753 (tt0) cc_final: 0.8133 (tm-30) REVERT: K 42 GLN cc_start: 0.8467 (mt0) cc_final: 0.8073 (mp10) REVERT: K 70 GLN cc_start: 0.8872 (mm110) cc_final: 0.8577 (mm110) REVERT: K 101 GLN cc_start: 0.8127 (pm20) cc_final: 0.7831 (pm20) REVERT: K 104 LYS cc_start: 0.8982 (tptp) cc_final: 0.8169 (tptp) REVERT: P 113 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8163 (p0) REVERT: P 362 MET cc_start: 0.8224 (ptp) cc_final: 0.7897 (ptm) outliers start: 45 outliers final: 35 residues processed: 366 average time/residue: 0.1265 time to fit residues: 71.1417 Evaluate side-chains 365 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 188 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046931 restraints weight = 61462.629| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.79 r_work: 0.2627 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21029 Z= 0.300 Angle : 0.724 9.178 28734 Z= 0.358 Chirality : 0.046 0.210 3354 Planarity : 0.004 0.041 3526 Dihedral : 6.981 47.504 4456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 2.82 % Allowed : 13.57 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.17), residues: 2477 helix: -1.02 (0.97), residues: 28 sheet: -0.37 (0.17), residues: 955 loop : -0.24 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 87 TYR 0.013 0.002 TYR E 80 PHE 0.018 0.002 PHE I 83 TRP 0.011 0.002 TRP M 178 HIS 0.004 0.001 HIS M 347 Details of bonding type rmsd covalent geometry : bond 0.00670 (20899) covalent geometry : angle 0.70119 (28388) SS BOND : bond 0.00391 ( 44) SS BOND : angle 0.45242 ( 88) hydrogen bonds : bond 0.03727 ( 643) hydrogen bonds : angle 6.50784 ( 1632) link_ALPHA1-2 : bond 0.00257 ( 4) link_ALPHA1-2 : angle 2.22557 ( 12) link_ALPHA1-3 : bond 0.00585 ( 8) link_ALPHA1-3 : angle 2.49117 ( 24) link_ALPHA1-6 : bond 0.00276 ( 10) link_ALPHA1-6 : angle 1.60795 ( 30) link_BETA1-4 : bond 0.00315 ( 40) link_BETA1-4 : angle 1.82388 ( 120) link_NAG-ASN : bond 0.00602 ( 24) link_NAG-ASN : angle 2.32399 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8554 (mm-30) REVERT: E 23 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8955 (tptp) REVERT: E 65 GLN cc_start: 0.8842 (tt0) cc_final: 0.8214 (mt0) REVERT: E 81 MET cc_start: 0.9437 (ttp) cc_final: 0.9107 (tmm) REVERT: E 82 GLU cc_start: 0.8817 (tt0) cc_final: 0.8075 (tm-30) REVERT: F 4 MET cc_start: 0.9130 (tpp) cc_final: 0.8713 (tpp) REVERT: F 42 GLN cc_start: 0.8582 (mt0) cc_final: 0.8050 (mp10) REVERT: F 70 GLN cc_start: 0.8819 (mm110) cc_final: 0.8543 (mm110) REVERT: F 101 GLN cc_start: 0.8200 (pm20) cc_final: 0.7893 (pm20) REVERT: F 104 LYS cc_start: 0.8979 (tptp) cc_final: 0.8115 (tptt) REVERT: M 113 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8180 (p0) REVERT: M 119 GLU cc_start: 0.9067 (mp0) cc_final: 0.8514 (mp0) REVERT: M 362 MET cc_start: 0.8313 (ptp) cc_final: 0.7985 (ptm) REVERT: G 10 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8571 (mm-30) REVERT: G 23 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9018 (tptp) REVERT: G 65 GLN cc_start: 0.8391 (tt0) cc_final: 0.7666 (mt0) REVERT: G 81 MET cc_start: 0.9418 (ttp) cc_final: 0.8939 (tmm) REVERT: G 82 GLU cc_start: 0.8777 (tt0) cc_final: 0.8140 (tm-30) REVERT: G 89 GLU cc_start: 0.9393 (pm20) cc_final: 0.9180 (pm20) REVERT: I 4 MET cc_start: 0.9166 (tpp) cc_final: 0.8704 (tpp) REVERT: I 24 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8295 (mtp85) REVERT: I 42 GLN cc_start: 0.8515 (mt0) cc_final: 0.8051 (mp10) REVERT: I 70 GLN cc_start: 0.8943 (mt0) cc_final: 0.8558 (mm110) REVERT: I 81 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8457 (tm-30) REVERT: I 101 GLN cc_start: 0.8220 (pm20) cc_final: 0.7896 (pm20) REVERT: N 113 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8201 (p0) REVERT: N 119 GLU cc_start: 0.9049 (mp0) cc_final: 0.8500 (mp0) REVERT: N 362 MET cc_start: 0.8317 (ptp) cc_final: 0.7990 (ptm) REVERT: H 10 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8573 (mm-30) REVERT: H 23 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9031 (tptp) REVERT: H 46 GLU cc_start: 0.8740 (tt0) cc_final: 0.8332 (tt0) REVERT: H 65 GLN cc_start: 0.8394 (tt0) cc_final: 0.8065 (mt0) REVERT: H 81 MET cc_start: 0.9426 (ttp) cc_final: 0.8892 (tmm) REVERT: H 82 GLU cc_start: 0.8781 (tt0) cc_final: 0.8124 (tm-30) REVERT: L 4 MET cc_start: 0.9133 (tpp) cc_final: 0.8727 (tpp) REVERT: L 42 GLN cc_start: 0.8524 (mt0) cc_final: 0.8106 (mp10) REVERT: L 70 GLN cc_start: 0.8846 (mm110) cc_final: 0.8546 (mm110) REVERT: L 81 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8399 (tm-30) REVERT: L 101 GLN cc_start: 0.8222 (pm20) cc_final: 0.7916 (pm20) REVERT: O 113 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8187 (p0) REVERT: O 119 GLU cc_start: 0.9057 (mp0) cc_final: 0.8510 (mp0) REVERT: O 362 MET cc_start: 0.8313 (ptp) cc_final: 0.7986 (ptm) REVERT: J 10 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8562 (mm-30) REVERT: J 23 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9028 (tptp) REVERT: J 46 GLU cc_start: 0.8574 (tt0) cc_final: 0.8233 (tt0) REVERT: J 63 LYS cc_start: 0.9537 (ptpp) cc_final: 0.9202 (ptpp) REVERT: J 65 GLN cc_start: 0.8404 (tt0) cc_final: 0.7679 (mt0) REVERT: J 81 MET cc_start: 0.9410 (ttp) cc_final: 0.9072 (tmm) REVERT: J 82 GLU cc_start: 0.8778 (tt0) cc_final: 0.8090 (tm-30) REVERT: K 4 MET cc_start: 0.9156 (tpp) cc_final: 0.8731 (tpp) REVERT: K 42 GLN cc_start: 0.8530 (mt0) cc_final: 0.8109 (mp10) REVERT: K 70 GLN cc_start: 0.8863 (mm110) cc_final: 0.8547 (mm110) REVERT: K 81 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8452 (tm-30) REVERT: K 101 GLN cc_start: 0.8207 (pm20) cc_final: 0.7884 (pm20) REVERT: P 113 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8188 (p0) REVERT: P 119 GLU cc_start: 0.9044 (mp0) cc_final: 0.8500 (mp0) REVERT: P 362 MET cc_start: 0.8310 (ptp) cc_final: 0.7986 (ptm) outliers start: 60 outliers final: 42 residues processed: 366 average time/residue: 0.1338 time to fit residues: 74.3720 Evaluate side-chains 373 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049115 restraints weight = 60890.803| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.78 r_work: 0.2667 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21029 Z= 0.183 Angle : 0.674 8.193 28734 Z= 0.336 Chirality : 0.045 0.213 3354 Planarity : 0.004 0.044 3526 Dihedral : 6.712 43.688 4456 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 2.54 % Allowed : 13.62 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.17), residues: 2477 helix: -0.99 (0.94), residues: 28 sheet: -0.30 (0.16), residues: 973 loop : -0.09 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 87 TYR 0.012 0.001 TYR M 121 PHE 0.027 0.002 PHE L 83 TRP 0.015 0.001 TRP M 178 HIS 0.003 0.001 HIS N 274 Details of bonding type rmsd covalent geometry : bond 0.00409 (20899) covalent geometry : angle 0.65696 (28388) SS BOND : bond 0.00259 ( 44) SS BOND : angle 0.40691 ( 88) hydrogen bonds : bond 0.03515 ( 643) hydrogen bonds : angle 6.38708 ( 1632) link_ALPHA1-2 : bond 0.00523 ( 4) link_ALPHA1-2 : angle 2.37757 ( 12) link_ALPHA1-3 : bond 0.00888 ( 8) link_ALPHA1-3 : angle 1.95685 ( 24) link_ALPHA1-6 : bond 0.00473 ( 10) link_ALPHA1-6 : angle 1.46414 ( 30) link_BETA1-4 : bond 0.00365 ( 40) link_BETA1-4 : angle 1.57180 ( 120) link_NAG-ASN : bond 0.00283 ( 24) link_NAG-ASN : angle 1.97426 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 329 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8542 (mm-30) REVERT: E 23 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8928 (tptp) REVERT: E 63 LYS cc_start: 0.9428 (ptpp) cc_final: 0.9209 (ptpp) REVERT: E 65 GLN cc_start: 0.8838 (tt0) cc_final: 0.8212 (mt0) REVERT: E 81 MET cc_start: 0.9401 (ttp) cc_final: 0.9120 (tmm) REVERT: E 82 GLU cc_start: 0.8810 (tt0) cc_final: 0.8108 (tm-30) REVERT: E 89 GLU cc_start: 0.9414 (pm20) cc_final: 0.9083 (pm20) REVERT: F 4 MET cc_start: 0.9116 (tpp) cc_final: 0.8752 (tpp) REVERT: F 42 GLN cc_start: 0.8543 (mt0) cc_final: 0.8034 (mp10) REVERT: F 70 GLN cc_start: 0.8808 (mm110) cc_final: 0.8484 (mm110) REVERT: F 101 GLN cc_start: 0.8144 (pm20) cc_final: 0.7822 (pm20) REVERT: M 113 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8211 (p0) REVERT: M 119 GLU cc_start: 0.9048 (mp0) cc_final: 0.8452 (mp0) REVERT: M 198 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: M 362 MET cc_start: 0.8229 (ptp) cc_final: 0.7907 (ptm) REVERT: G 10 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8575 (mm-30) REVERT: G 23 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9014 (tptp) REVERT: G 63 LYS cc_start: 0.9428 (ptpp) cc_final: 0.9205 (ptpp) REVERT: G 65 GLN cc_start: 0.8394 (tt0) cc_final: 0.7686 (mt0) REVERT: G 81 MET cc_start: 0.9389 (ttp) cc_final: 0.8961 (tmm) REVERT: G 82 GLU cc_start: 0.8764 (tt0) cc_final: 0.8134 (tm-30) REVERT: G 89 GLU cc_start: 0.9390 (pm20) cc_final: 0.9181 (pm20) REVERT: I 4 MET cc_start: 0.9145 (tpp) cc_final: 0.8717 (tpp) REVERT: I 42 GLN cc_start: 0.8511 (mt0) cc_final: 0.8111 (mp10) REVERT: I 70 GLN cc_start: 0.8925 (mt0) cc_final: 0.8643 (mm110) REVERT: I 81 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8378 (tm-30) REVERT: I 101 GLN cc_start: 0.8205 (pm20) cc_final: 0.7892 (pm20) REVERT: I 104 LYS cc_start: 0.8765 (tptp) cc_final: 0.8502 (tptt) REVERT: N 113 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8215 (p0) REVERT: N 119 GLU cc_start: 0.9041 (mp0) cc_final: 0.8456 (mp0) REVERT: N 362 MET cc_start: 0.8210 (ptp) cc_final: 0.7882 (ptm) REVERT: H 10 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8562 (mm-30) REVERT: H 23 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9000 (tptp) REVERT: H 46 GLU cc_start: 0.8680 (tt0) cc_final: 0.8307 (tt0) REVERT: H 65 GLN cc_start: 0.8367 (tt0) cc_final: 0.7724 (mt0) REVERT: H 81 MET cc_start: 0.9421 (ttp) cc_final: 0.8964 (tmm) REVERT: H 82 GLU cc_start: 0.8749 (tt0) cc_final: 0.8116 (tm-30) REVERT: L 42 GLN cc_start: 0.8495 (mt0) cc_final: 0.8095 (mp10) REVERT: L 70 GLN cc_start: 0.8892 (mm110) cc_final: 0.8648 (mm110) REVERT: L 81 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8338 (tm-30) REVERT: L 101 GLN cc_start: 0.8167 (pm20) cc_final: 0.7854 (pm20) REVERT: L 106 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7903 (mp0) REVERT: O 113 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8194 (p0) REVERT: O 119 GLU cc_start: 0.9042 (mp0) cc_final: 0.8459 (mp0) REVERT: O 362 MET cc_start: 0.8213 (ptp) cc_final: 0.7881 (ptm) REVERT: J 10 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8565 (mm-30) REVERT: J 23 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9000 (tptp) REVERT: J 46 GLU cc_start: 0.8587 (tt0) cc_final: 0.8185 (tt0) REVERT: J 63 LYS cc_start: 0.9515 (ptpp) cc_final: 0.9175 (ptpp) REVERT: J 65 GLN cc_start: 0.8398 (tt0) cc_final: 0.7682 (mt0) REVERT: J 81 MET cc_start: 0.9386 (ttp) cc_final: 0.8944 (tmm) REVERT: J 82 GLU cc_start: 0.8759 (tt0) cc_final: 0.8127 (tm-30) REVERT: K 4 MET cc_start: 0.9167 (tpp) cc_final: 0.8757 (tpp) REVERT: K 42 GLN cc_start: 0.8526 (mt0) cc_final: 0.8123 (mp10) REVERT: K 70 GLN cc_start: 0.8871 (mm110) cc_final: 0.8596 (mm110) REVERT: K 81 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8393 (tm-30) REVERT: K 101 GLN cc_start: 0.8199 (pm20) cc_final: 0.7885 (pm20) REVERT: P 113 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8196 (p0) REVERT: P 119 GLU cc_start: 0.9032 (mp0) cc_final: 0.8451 (mp0) REVERT: P 362 MET cc_start: 0.8231 (ptp) cc_final: 0.7913 (ptm) outliers start: 54 outliers final: 43 residues processed: 361 average time/residue: 0.1301 time to fit residues: 71.6184 Evaluate side-chains 369 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 169 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049062 restraints weight = 60974.630| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.80 r_work: 0.2662 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21029 Z= 0.199 Angle : 0.683 8.381 28734 Z= 0.340 Chirality : 0.045 0.218 3354 Planarity : 0.004 0.043 3526 Dihedral : 6.665 43.233 4456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 2.58 % Allowed : 13.43 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.35 (0.17), residues: 2477 helix: -0.80 (0.98), residues: 28 sheet: -0.35 (0.17), residues: 941 loop : -0.03 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 87 TYR 0.011 0.001 TYR M 121 PHE 0.029 0.002 PHE L 83 TRP 0.014 0.001 TRP M 178 HIS 0.003 0.001 HIS N 274 Details of bonding type rmsd covalent geometry : bond 0.00447 (20899) covalent geometry : angle 0.66608 (28388) SS BOND : bond 0.00271 ( 44) SS BOND : angle 0.38203 ( 88) hydrogen bonds : bond 0.03546 ( 643) hydrogen bonds : angle 6.39244 ( 1632) link_ALPHA1-2 : bond 0.00440 ( 4) link_ALPHA1-2 : angle 2.22913 ( 12) link_ALPHA1-3 : bond 0.00773 ( 8) link_ALPHA1-3 : angle 2.08078 ( 24) link_ALPHA1-6 : bond 0.00418 ( 10) link_ALPHA1-6 : angle 1.50683 ( 30) link_BETA1-4 : bond 0.00328 ( 40) link_BETA1-4 : angle 1.55924 ( 120) link_NAG-ASN : bond 0.00361 ( 24) link_NAG-ASN : angle 2.00316 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8609 (mm-30) REVERT: E 23 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8925 (tptp) REVERT: E 63 LYS cc_start: 0.9441 (ptpp) cc_final: 0.9217 (ptpp) REVERT: E 65 GLN cc_start: 0.8853 (tt0) cc_final: 0.8224 (mt0) REVERT: E 81 MET cc_start: 0.9433 (ttp) cc_final: 0.9077 (tmm) REVERT: E 82 GLU cc_start: 0.8819 (tt0) cc_final: 0.8123 (tm-30) REVERT: E 87 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: E 89 GLU cc_start: 0.9435 (pm20) cc_final: 0.9128 (pm20) REVERT: F 4 MET cc_start: 0.9123 (tpp) cc_final: 0.8778 (tpp) REVERT: F 42 GLN cc_start: 0.8529 (mt0) cc_final: 0.8078 (mp10) REVERT: F 70 GLN cc_start: 0.8812 (mm110) cc_final: 0.8535 (mm110) REVERT: F 101 GLN cc_start: 0.8153 (pm20) cc_final: 0.7815 (pm20) REVERT: F 104 LYS cc_start: 0.8783 (tptp) cc_final: 0.8074 (tptp) REVERT: M 113 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8234 (p0) REVERT: M 119 GLU cc_start: 0.9055 (mp0) cc_final: 0.8459 (mp0) REVERT: M 198 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8720 (m-30) REVERT: M 362 MET cc_start: 0.8236 (ptp) cc_final: 0.7901 (ptm) REVERT: G 10 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8632 (mm-30) REVERT: G 23 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8994 (tptp) REVERT: G 46 GLU cc_start: 0.8424 (tt0) cc_final: 0.8180 (tt0) REVERT: G 63 LYS cc_start: 0.9441 (ptpp) cc_final: 0.9205 (ptpp) REVERT: G 65 GLN cc_start: 0.8404 (tt0) cc_final: 0.7905 (tt0) REVERT: G 81 MET cc_start: 0.9417 (ttp) cc_final: 0.8926 (tmm) REVERT: G 82 GLU cc_start: 0.8774 (tt0) cc_final: 0.8174 (tm-30) REVERT: G 89 GLU cc_start: 0.9364 (pm20) cc_final: 0.9143 (pm20) REVERT: I 4 MET cc_start: 0.9154 (tpp) cc_final: 0.8791 (tpp) REVERT: I 24 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8227 (mtp85) REVERT: I 42 GLN cc_start: 0.8513 (mt0) cc_final: 0.8082 (mp10) REVERT: I 70 GLN cc_start: 0.8941 (mt0) cc_final: 0.8646 (mm110) REVERT: I 81 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8389 (tm-30) REVERT: I 101 GLN cc_start: 0.8202 (pm20) cc_final: 0.7883 (pm20) REVERT: N 113 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8248 (p0) REVERT: N 119 GLU cc_start: 0.9034 (mp0) cc_final: 0.8425 (mp0) REVERT: N 362 MET cc_start: 0.8239 (ptp) cc_final: 0.7910 (ptm) REVERT: H 10 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8630 (mm-30) REVERT: H 23 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9009 (tptp) REVERT: H 46 GLU cc_start: 0.8714 (tt0) cc_final: 0.8341 (tt0) REVERT: H 65 GLN cc_start: 0.8371 (tt0) cc_final: 0.7711 (mt0) REVERT: H 81 MET cc_start: 0.9411 (ttp) cc_final: 0.8955 (tmm) REVERT: H 82 GLU cc_start: 0.8763 (tt0) cc_final: 0.8169 (tm-30) REVERT: L 4 MET cc_start: 0.9148 (tpp) cc_final: 0.8760 (tpp) REVERT: L 42 GLN cc_start: 0.8520 (mt0) cc_final: 0.8133 (mp10) REVERT: L 70 GLN cc_start: 0.8893 (mm110) cc_final: 0.8618 (mm110) REVERT: L 101 GLN cc_start: 0.8149 (pm20) cc_final: 0.7827 (pm20) REVERT: O 113 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8240 (p0) REVERT: O 119 GLU cc_start: 0.9041 (mp0) cc_final: 0.8438 (mp0) REVERT: O 362 MET cc_start: 0.8230 (ptp) cc_final: 0.7895 (ptm) REVERT: J 10 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8581 (mm-30) REVERT: J 19 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8981 (mmm160) REVERT: J 23 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9008 (tptp) REVERT: J 46 GLU cc_start: 0.8624 (tt0) cc_final: 0.8202 (tt0) REVERT: J 63 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9163 (ptpp) REVERT: J 65 GLN cc_start: 0.8442 (tt0) cc_final: 0.7946 (tt0) REVERT: J 81 MET cc_start: 0.9404 (ttp) cc_final: 0.8909 (tmm) REVERT: J 82 GLU cc_start: 0.8769 (tt0) cc_final: 0.8166 (tm-30) REVERT: K 4 MET cc_start: 0.9165 (tpp) cc_final: 0.8778 (tpp) REVERT: K 42 GLN cc_start: 0.8529 (mt0) cc_final: 0.8093 (mp10) REVERT: K 70 GLN cc_start: 0.8875 (mm110) cc_final: 0.8603 (mm110) REVERT: K 81 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8378 (tm-30) REVERT: K 101 GLN cc_start: 0.8188 (pm20) cc_final: 0.7871 (pm20) REVERT: P 113 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8216 (p0) REVERT: P 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.8429 (mp0) REVERT: P 362 MET cc_start: 0.8233 (ptp) cc_final: 0.7903 (ptm) outliers start: 55 outliers final: 42 residues processed: 348 average time/residue: 0.1310 time to fit residues: 70.1322 Evaluate side-chains 367 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049237 restraints weight = 62003.687| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.81 r_work: 0.2631 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21029 Z= 0.285 Angle : 0.729 8.879 28734 Z= 0.362 Chirality : 0.046 0.217 3354 Planarity : 0.005 0.060 3526 Dihedral : 6.869 44.906 4456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 2.68 % Allowed : 14.00 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.44 (0.17), residues: 2477 helix: -0.64 (1.02), residues: 28 sheet: -0.25 (0.17), residues: 944 loop : -0.22 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 87 TYR 0.012 0.002 TYR M 121 PHE 0.026 0.002 PHE L 83 TRP 0.011 0.001 TRP L 35 HIS 0.003 0.001 HIS M 347 Details of bonding type rmsd covalent geometry : bond 0.00639 (20899) covalent geometry : angle 0.70951 (28388) SS BOND : bond 0.00339 ( 44) SS BOND : angle 0.45116 ( 88) hydrogen bonds : bond 0.03738 ( 643) hydrogen bonds : angle 6.42241 ( 1632) link_ALPHA1-2 : bond 0.00276 ( 4) link_ALPHA1-2 : angle 2.26313 ( 12) link_ALPHA1-3 : bond 0.00606 ( 8) link_ALPHA1-3 : angle 2.42605 ( 24) link_ALPHA1-6 : bond 0.00285 ( 10) link_ALPHA1-6 : angle 1.60454 ( 30) link_BETA1-4 : bond 0.00304 ( 40) link_BETA1-4 : angle 1.64226 ( 120) link_NAG-ASN : bond 0.00578 ( 24) link_NAG-ASN : angle 2.24813 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8603 (mm-30) REVERT: E 23 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8941 (tptp) REVERT: E 46 GLU cc_start: 0.8545 (tt0) cc_final: 0.8256 (tt0) REVERT: E 63 LYS cc_start: 0.9452 (ptpp) cc_final: 0.9234 (ptpp) REVERT: E 65 GLN cc_start: 0.8885 (tt0) cc_final: 0.8248 (mt0) REVERT: E 81 MET cc_start: 0.9505 (ttp) cc_final: 0.9060 (tmm) REVERT: E 82 GLU cc_start: 0.8861 (tt0) cc_final: 0.8146 (tm-30) REVERT: F 42 GLN cc_start: 0.8575 (mt0) cc_final: 0.8078 (mp10) REVERT: F 70 GLN cc_start: 0.8858 (mm110) cc_final: 0.8602 (mm110) REVERT: F 101 GLN cc_start: 0.8187 (pm20) cc_final: 0.7843 (pm20) REVERT: M 113 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8228 (p0) REVERT: M 119 GLU cc_start: 0.9082 (mp0) cc_final: 0.8478 (mp0) REVERT: M 362 MET cc_start: 0.8297 (ptp) cc_final: 0.7976 (ptm) REVERT: G 10 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8584 (mm-30) REVERT: G 23 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9008 (tptp) REVERT: G 46 GLU cc_start: 0.8440 (tt0) cc_final: 0.8115 (tt0) REVERT: G 63 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9218 (ptpp) REVERT: G 65 GLN cc_start: 0.8439 (tt0) cc_final: 0.7948 (tt0) REVERT: G 81 MET cc_start: 0.9464 (ttp) cc_final: 0.9004 (tmm) REVERT: G 82 GLU cc_start: 0.8796 (tt0) cc_final: 0.8170 (tm-30) REVERT: G 89 GLU cc_start: 0.9361 (pm20) cc_final: 0.9147 (pm20) REVERT: I 4 MET cc_start: 0.9120 (tpp) cc_final: 0.8727 (tpp) REVERT: I 24 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8218 (mtp85) REVERT: I 27 ARG cc_start: 0.9087 (ptt90) cc_final: 0.8702 (ptt180) REVERT: I 42 GLN cc_start: 0.8566 (mt0) cc_final: 0.8116 (mp10) REVERT: I 70 GLN cc_start: 0.8907 (mt0) cc_final: 0.8583 (mm110) REVERT: I 101 GLN cc_start: 0.8224 (pm20) cc_final: 0.7904 (pm20) REVERT: N 113 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8246 (p0) REVERT: N 362 MET cc_start: 0.8291 (ptp) cc_final: 0.7973 (ptm) REVERT: H 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8593 (mm-30) REVERT: H 19 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.9156 (mmm-85) REVERT: H 23 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9030 (tptp) REVERT: H 46 GLU cc_start: 0.8811 (tt0) cc_final: 0.8428 (tt0) REVERT: H 65 GLN cc_start: 0.8451 (tt0) cc_final: 0.7984 (tt0) REVERT: H 81 MET cc_start: 0.9471 (ttp) cc_final: 0.9039 (tmm) REVERT: H 82 GLU cc_start: 0.8817 (tt0) cc_final: 0.8147 (tm-30) REVERT: L 4 MET cc_start: 0.9135 (tpp) cc_final: 0.8725 (tpp) REVERT: L 42 GLN cc_start: 0.8556 (mt0) cc_final: 0.8100 (mp10) REVERT: L 70 GLN cc_start: 0.8862 (mm110) cc_final: 0.8590 (mm110) REVERT: L 101 GLN cc_start: 0.8192 (pm20) cc_final: 0.7863 (pm20) REVERT: L 104 LYS cc_start: 0.8640 (tptp) cc_final: 0.8304 (tptp) REVERT: L 106 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: O 113 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8241 (p0) REVERT: O 362 MET cc_start: 0.8307 (ptp) cc_final: 0.7977 (ptm) REVERT: J 10 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8587 (mm-30) REVERT: J 23 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9013 (tptp) REVERT: J 46 GLU cc_start: 0.8739 (tt0) cc_final: 0.8292 (tt0) REVERT: J 63 LYS cc_start: 0.9520 (ptpp) cc_final: 0.9175 (ptpp) REVERT: J 65 GLN cc_start: 0.8501 (tt0) cc_final: 0.8018 (tt0) REVERT: J 81 MET cc_start: 0.9455 (ttp) cc_final: 0.8995 (tmm) REVERT: J 82 GLU cc_start: 0.8792 (tt0) cc_final: 0.8167 (tm-30) REVERT: K 42 GLN cc_start: 0.8570 (mt0) cc_final: 0.8122 (mp10) REVERT: K 70 GLN cc_start: 0.8864 (mm110) cc_final: 0.8573 (mm110) REVERT: K 79 GLN cc_start: 0.9254 (mm110) cc_final: 0.8896 (mp10) REVERT: K 101 GLN cc_start: 0.8221 (pm20) cc_final: 0.7893 (pm20) REVERT: P 113 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8226 (p0) REVERT: P 148 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (p) REVERT: P 362 MET cc_start: 0.8306 (ptp) cc_final: 0.7977 (ptm) outliers start: 57 outliers final: 45 residues processed: 346 average time/residue: 0.1287 time to fit residues: 68.3019 Evaluate side-chains 368 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 0.0770 chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.050162 restraints weight = 60609.699| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.81 r_work: 0.2697 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21029 Z= 0.138 Angle : 0.674 7.462 28734 Z= 0.336 Chirality : 0.044 0.217 3354 Planarity : 0.004 0.072 3526 Dihedral : 6.447 43.872 4456 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 2.40 % Allowed : 14.37 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2477 helix: -0.86 (0.94), residues: 28 sheet: -0.20 (0.17), residues: 924 loop : 0.01 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 87 TYR 0.012 0.001 TYR E 32 PHE 0.020 0.001 PHE L 83 TRP 0.019 0.002 TRP M 178 HIS 0.003 0.001 HIS O 274 Details of bonding type rmsd covalent geometry : bond 0.00312 (20899) covalent geometry : angle 0.66092 (28388) SS BOND : bond 0.00199 ( 44) SS BOND : angle 0.38000 ( 88) hydrogen bonds : bond 0.03400 ( 643) hydrogen bonds : angle 6.23590 ( 1632) link_ALPHA1-2 : bond 0.00637 ( 4) link_ALPHA1-2 : angle 2.30225 ( 12) link_ALPHA1-3 : bond 0.01052 ( 8) link_ALPHA1-3 : angle 1.68831 ( 24) link_ALPHA1-6 : bond 0.00583 ( 10) link_ALPHA1-6 : angle 1.39502 ( 30) link_BETA1-4 : bond 0.00404 ( 40) link_BETA1-4 : angle 1.38555 ( 120) link_NAG-ASN : bond 0.00143 ( 24) link_NAG-ASN : angle 1.71516 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.66 seconds wall clock time: 67 minutes 45.68 seconds (4065.68 seconds total)