Starting phenix.real_space_refine on Wed Jun 18 03:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g30_29686/06_2025/8g30_29686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g30_29686/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g30_29686/06_2025/8g30_29686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g30_29686/06_2025/8g30_29686.map" model { file = "/net/cci-nas-00/data/ceres_data/8g30_29686/06_2025/8g30_29686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g30_29686/06_2025/8g30_29686.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.51, per 1000 atoms: 0.71 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: 7.91 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.85 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: 11.78 Time building geometry restraints manager: 7.95 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 469 or resid 501)) selection = (chain 'N' and (resid 82 through 244 or resid 250 through 469 or resid 2000)) selection = (chain 'O' and (resid 82 through 244 or resid 250 through 469 or resid 2000)) selection = (chain 'P' and (resid 82 through 244 or resid 250 through 469 or resid 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: 14.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 58.810 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 TRP 0.081 0.016 TRP M 458 HIS 0.024 0.005 HIS N 168 PHE 0.087 0.013 PHE O 205 TYR 0.116 0.016 TYR N 121 ARG 0.030 0.003 ARG M 224 Details of bonding type rmsd link_NAG-ASN : bond 0.02409 ( 24) link_NAG-ASN : angle 5.86405 ( 72) 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_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) hydrogen bonds : bond 0.14365 ( 643) hydrogen bonds : angle 8.61819 ( 1632) SS BOND : bond 0.03542 ( 44) SS BOND : angle 2.31605 ( 88) covalent geometry : bond 0.01577 (20899) covalent geometry : angle 1.86663 (28388) *********************** 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 : 2.181 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 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: 0.8998 (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: 0.3917 time to fit residues: 257.9923 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 : 2.901 ------------------------------------------------------------------------------- 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 206 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 G 62 GLN N 147 ASN H 62 GLN O 147 ASN J 62 GLN P 147 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051175 restraints weight = 60651.766| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.83 r_work: 0.2638 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21029 Z= 0.207 Angle : 0.806 7.206 28734 Z= 0.409 Chirality : 0.049 0.175 3354 Planarity : 0.004 0.036 3526 Dihedral : 13.135 79.390 4472 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 0.80 % Allowed : 10.52 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2477 helix: -2.35 (0.77), residues: 28 sheet: -0.15 (0.18), residues: 886 loop : -0.76 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 115 HIS 0.003 0.001 HIS M 168 PHE 0.017 0.002 PHE I 83 TYR 0.018 0.002 TYR P 121 ARG 0.006 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 24) link_NAG-ASN : angle 2.91160 ( 72) link_ALPHA1-6 : bond 0.00733 ( 10) link_ALPHA1-6 : angle 1.29973 ( 30) link_BETA1-4 : bond 0.00543 ( 40) link_BETA1-4 : angle 2.71843 ( 120) link_ALPHA1-2 : bond 0.00674 ( 4) link_ALPHA1-2 : angle 2.05557 ( 12) link_ALPHA1-3 : bond 0.01127 ( 8) link_ALPHA1-3 : angle 2.17598 ( 24) hydrogen bonds : bond 0.04720 ( 643) hydrogen bonds : angle 7.41492 ( 1632) SS BOND : bond 0.00433 ( 44) SS BOND : angle 0.73540 ( 88) covalent geometry : bond 0.00450 (20899) covalent geometry : angle 0.77170 (28388) *********************** 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 398 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 381 time to evaluate : 2.303 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: E 23 LYS cc_start: 0.9191 (tptm) cc_final: 0.8965 (tptp) REVERT: E 31 LYS cc_start: 0.8687 (tttp) cc_final: 0.8309 (tttm) REVERT: E 65 GLN cc_start: 0.8226 (tt0) cc_final: 0.7764 (mt0) REVERT: E 81 MET cc_start: 0.9400 (ttp) cc_final: 0.8477 (tmm) REVERT: E 82 GLU cc_start: 0.8535 (tt0) cc_final: 0.7951 (tm-30) REVERT: E 89 GLU cc_start: 0.9553 (mp0) cc_final: 0.9286 (pm20) REVERT: F 42 GLN cc_start: 0.8049 (mt0) cc_final: 0.7809 (mp10) REVERT: F 48 ILE cc_start: 0.8944 (mm) cc_final: 0.8724 (mm) REVERT: F 54 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: F 70 GLN cc_start: 0.8688 (mm110) cc_final: 0.8325 (mm110) REVERT: F 79 GLN cc_start: 0.9206 (mm110) cc_final: 0.8844 (mp10) REVERT: F 83 PHE cc_start: 0.7376 (m-80) cc_final: 0.7057 (m-80) REVERT: M 113 ASP cc_start: 0.8737 (p0) cc_final: 0.8419 (p0) REVERT: M 119 GLU cc_start: 0.9055 (mp0) cc_final: 0.8300 (mp0) REVERT: G 3 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8202 (mm-40) REVERT: G 23 LYS cc_start: 0.9223 (tptm) cc_final: 0.8979 (tptp) REVERT: G 65 GLN cc_start: 0.7894 (tt0) cc_final: 0.7592 (mt0) REVERT: G 81 MET cc_start: 0.9380 (ttp) cc_final: 0.8501 (tmm) REVERT: G 82 GLU cc_start: 0.8546 (tt0) cc_final: 0.7979 (tm-30) REVERT: I 42 GLN cc_start: 0.8114 (mt0) cc_final: 0.7872 (mp10) REVERT: I 54 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: I 70 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: I 79 GLN cc_start: 0.9194 (mm110) cc_final: 0.8732 (mm110) REVERT: I 89 GLN cc_start: 0.9355 (tm-30) cc_final: 0.9137 (tt0) REVERT: N 113 ASP cc_start: 0.8692 (p0) cc_final: 0.8353 (p0) REVERT: N 119 GLU cc_start: 0.9112 (mp0) cc_final: 0.8276 (mp0) REVERT: N 402 ASN cc_start: 0.8308 (m-40) cc_final: 0.8099 (m-40) REVERT: H 3 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8198 (mm-40) REVERT: H 23 LYS cc_start: 0.9220 (tptm) cc_final: 0.8974 (tptp) REVERT: H 65 GLN cc_start: 0.7882 (tt0) cc_final: 0.7578 (mt0) REVERT: H 81 MET cc_start: 0.9371 (ttp) cc_final: 0.8481 (tmm) REVERT: H 82 GLU cc_start: 0.8532 (tt0) cc_final: 0.7962 (tm-30) REVERT: L 42 GLN cc_start: 0.8138 (mt0) cc_final: 0.7888 (mp10) REVERT: L 54 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7626 (mtm-85) REVERT: L 70 GLN cc_start: 0.8699 (mm110) cc_final: 0.8409 (mm110) REVERT: L 79 GLN cc_start: 0.9193 (mm110) cc_final: 0.8724 (mm110) REVERT: O 113 ASP cc_start: 0.8696 (p0) cc_final: 0.8357 (p0) REVERT: O 119 GLU cc_start: 0.9100 (mp0) cc_final: 0.8265 (mp0) REVERT: O 402 ASN cc_start: 0.8300 (m-40) cc_final: 0.8089 (m-40) REVERT: J 3 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8202 (mm-40) REVERT: J 23 LYS cc_start: 0.9228 (tptm) cc_final: 0.8983 (tptp) REVERT: J 65 GLN cc_start: 0.7897 (tt0) cc_final: 0.7589 (mt0) REVERT: J 81 MET cc_start: 0.9380 (ttp) cc_final: 0.8503 (tmm) REVERT: J 82 GLU cc_start: 0.8540 (tt0) cc_final: 0.7977 (tm-30) REVERT: K 42 GLN cc_start: 0.8108 (mt0) cc_final: 0.7868 (mp10) REVERT: K 54 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: K 70 GLN cc_start: 0.8655 (mm110) cc_final: 0.8345 (mm110) REVERT: K 89 GLN cc_start: 0.9354 (tm-30) cc_final: 0.9116 (tt0) REVERT: K 106 GLU cc_start: 0.8044 (tp30) cc_final: 0.7781 (tm-30) REVERT: K 107 ILE cc_start: 0.9400 (mp) cc_final: 0.9182 (pt) REVERT: P 113 ASP cc_start: 0.8707 (p0) cc_final: 0.8368 (p0) REVERT: P 119 GLU cc_start: 0.9094 (mp0) cc_final: 0.8266 (mp0) outliers start: 17 outliers final: 15 residues processed: 389 average time/residue: 0.4285 time to fit residues: 244.6124 Evaluate side-chains 350 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 334 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU 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 34 LEU 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 34 LEU 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 34 LEU 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 116 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 347 HIS N 347 HIS O 347 HIS P 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.046565 restraints weight = 62099.486| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.76 r_work: 0.2606 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 21029 Z= 0.308 Angle : 0.789 8.540 28734 Z= 0.388 Chirality : 0.048 0.157 3354 Planarity : 0.005 0.049 3526 Dihedral : 10.020 60.787 4464 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 1.93 % Allowed : 11.55 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2477 helix: -1.56 (0.93), residues: 28 sheet: -0.24 (0.18), residues: 890 loop : -0.55 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 115 HIS 0.004 0.001 HIS M 168 PHE 0.017 0.002 PHE M 410 TYR 0.020 0.002 TYR M 121 ARG 0.008 0.001 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 24) link_NAG-ASN : angle 2.63084 ( 72) link_ALPHA1-6 : bond 0.00361 ( 10) link_ALPHA1-6 : angle 1.59840 ( 30) link_BETA1-4 : bond 0.00424 ( 40) link_BETA1-4 : angle 2.63778 ( 120) link_ALPHA1-2 : bond 0.00266 ( 4) link_ALPHA1-2 : angle 2.29978 ( 12) link_ALPHA1-3 : bond 0.00362 ( 8) link_ALPHA1-3 : angle 2.51283 ( 24) hydrogen bonds : bond 0.04214 ( 643) hydrogen bonds : angle 6.91785 ( 1632) SS BOND : bond 0.00437 ( 44) SS BOND : angle 0.57414 ( 88) covalent geometry : bond 0.00685 (20899) covalent geometry : angle 0.75644 (28388) *********************** 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 386 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 2.208 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 23 LYS cc_start: 0.9209 (tptm) cc_final: 0.8912 (tptp) REVERT: E 65 GLN cc_start: 0.8452 (tt0) cc_final: 0.7900 (mt0) REVERT: E 81 MET cc_start: 0.9394 (ttp) cc_final: 0.8646 (tmm) REVERT: E 82 GLU cc_start: 0.8639 (tt0) cc_final: 0.7989 (tm-30) REVERT: F 42 GLN cc_start: 0.8314 (mt0) cc_final: 0.7955 (mp10) REVERT: F 54 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7858 (mtm-85) REVERT: F 70 GLN cc_start: 0.8598 (mm110) cc_final: 0.8224 (mm110) REVERT: M 113 ASP cc_start: 0.8822 (p0) cc_final: 0.8344 (p0) REVERT: M 119 GLU cc_start: 0.9126 (mp0) cc_final: 0.8455 (mp0) REVERT: M 362 MET cc_start: 0.8160 (ptp) cc_final: 0.7791 (ptm) REVERT: G 23 LYS cc_start: 0.9208 (tptm) cc_final: 0.8906 (tptp) REVERT: G 46 GLU cc_start: 0.8483 (tt0) cc_final: 0.8157 (tt0) REVERT: G 65 GLN cc_start: 0.8098 (tt0) cc_final: 0.7725 (mt0) REVERT: G 81 MET cc_start: 0.9384 (ttp) cc_final: 0.8954 (tmm) REVERT: G 82 GLU cc_start: 0.8633 (tt0) cc_final: 0.7911 (tm-30) REVERT: I 42 GLN cc_start: 0.8324 (mt0) cc_final: 0.7961 (mp10) REVERT: I 70 GLN cc_start: 0.8762 (mt0) cc_final: 0.8210 (mm-40) REVERT: N 113 ASP cc_start: 0.8782 (p0) cc_final: 0.8293 (p0) REVERT: N 119 GLU cc_start: 0.9133 (mp0) cc_final: 0.8421 (mp0) REVERT: N 362 MET cc_start: 0.8155 (ptp) cc_final: 0.7796 (ptm) REVERT: H 23 LYS cc_start: 0.9191 (tptm) cc_final: 0.8887 (tptp) REVERT: H 65 GLN cc_start: 0.8192 (tt0) cc_final: 0.7848 (mt0) REVERT: H 81 MET cc_start: 0.9384 (ttp) cc_final: 0.8958 (tmm) REVERT: H 82 GLU cc_start: 0.8628 (tt0) cc_final: 0.7904 (tm-30) REVERT: L 4 MET cc_start: 0.8979 (tpp) cc_final: 0.8546 (tpp) REVERT: L 42 GLN cc_start: 0.8334 (mt0) cc_final: 0.7967 (mp10) REVERT: L 70 GLN cc_start: 0.8700 (mm110) cc_final: 0.8242 (mm-40) REVERT: L 101 GLN cc_start: 0.7916 (pm20) cc_final: 0.7671 (pm20) REVERT: O 113 ASP cc_start: 0.8788 (p0) cc_final: 0.8282 (p0) REVERT: O 119 GLU cc_start: 0.9121 (mp0) cc_final: 0.8413 (mp0) REVERT: O 362 MET cc_start: 0.8163 (ptp) cc_final: 0.7787 (ptm) REVERT: J 23 LYS cc_start: 0.9204 (tptm) cc_final: 0.8905 (tptp) REVERT: J 46 GLU cc_start: 0.8486 (tt0) cc_final: 0.8167 (tt0) REVERT: J 65 GLN cc_start: 0.8088 (tt0) cc_final: 0.7716 (mt0) REVERT: J 81 MET cc_start: 0.9380 (ttp) cc_final: 0.8949 (tmm) REVERT: J 82 GLU cc_start: 0.8627 (tt0) cc_final: 0.7903 (tm-30) REVERT: K 42 GLN cc_start: 0.8331 (mt0) cc_final: 0.7964 (mp10) REVERT: K 70 GLN cc_start: 0.8657 (mm110) cc_final: 0.8319 (mm110) REVERT: P 113 ASP cc_start: 0.8789 (p0) cc_final: 0.7940 (p0) REVERT: P 119 GLU cc_start: 0.9124 (mp0) cc_final: 0.8418 (mp0) REVERT: P 362 MET cc_start: 0.8154 (ptp) cc_final: 0.7784 (ptm) outliers start: 41 outliers final: 41 residues processed: 364 average time/residue: 0.4236 time to fit residues: 233.8844 Evaluate side-chains 362 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 5.311 ------------------------------------------------------------------------------- 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 M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL 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 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 109 SER 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 34 LEU Chi-restraints excluded: chain H residue 54 ILE 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 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 34 LEU Chi-restraints excluded: chain J residue 54 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.066611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052094 restraints weight = 59538.363| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.83 r_work: 0.2683 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21029 Z= 0.134 Angle : 0.677 8.700 28734 Z= 0.334 Chirality : 0.045 0.187 3354 Planarity : 0.004 0.037 3526 Dihedral : 7.997 50.675 4464 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.27 % Allowed : 12.64 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2477 helix: -1.97 (0.77), residues: 28 sheet: -0.27 (0.17), residues: 921 loop : -0.28 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 115 HIS 0.003 0.001 HIS N 274 PHE 0.024 0.002 PHE F 83 TYR 0.014 0.001 TYR M 121 ARG 0.008 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 24) link_NAG-ASN : angle 1.99277 ( 72) link_ALPHA1-6 : bond 0.00655 ( 10) link_ALPHA1-6 : angle 1.37163 ( 30) link_BETA1-4 : bond 0.00486 ( 40) link_BETA1-4 : angle 2.20495 ( 120) link_ALPHA1-2 : bond 0.00792 ( 4) link_ALPHA1-2 : angle 2.30076 ( 12) link_ALPHA1-3 : bond 0.01088 ( 8) link_ALPHA1-3 : angle 1.70732 ( 24) hydrogen bonds : bond 0.03542 ( 643) hydrogen bonds : angle 6.65135 ( 1632) SS BOND : bond 0.00237 ( 44) SS BOND : angle 0.46238 ( 88) covalent geometry : bond 0.00290 (20899) covalent geometry : angle 0.65217 (28388) *********************** 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 394 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 367 time to evaluate : 2.487 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: 0.8831 (mm-30) cc_final: 0.8467 (mm-30) REVERT: E 23 LYS cc_start: 0.9276 (tptm) cc_final: 0.9017 (tptm) REVERT: E 46 GLU cc_start: 0.8620 (tt0) cc_final: 0.8411 (tt0) REVERT: E 65 GLN cc_start: 0.8610 (tt0) cc_final: 0.8120 (mt0) REVERT: E 73 ASP cc_start: 0.7857 (t0) cc_final: 0.7636 (t0) REVERT: E 81 MET cc_start: 0.9349 (ttp) cc_final: 0.9066 (tmm) REVERT: E 82 GLU cc_start: 0.8700 (tt0) cc_final: 0.8005 (tm-30) REVERT: F 4 MET cc_start: 0.9186 (tpp) cc_final: 0.8725 (tpp) REVERT: F 42 GLN cc_start: 0.8373 (mt0) cc_final: 0.7966 (mp10) REVERT: F 54 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: F 70 GLN cc_start: 0.8790 (mm110) cc_final: 0.8495 (mm110) REVERT: F 104 LYS cc_start: 0.9047 (tptp) cc_final: 0.8837 (tptp) REVERT: M 113 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8032 (p0) REVERT: M 119 GLU cc_start: 0.9049 (mp0) cc_final: 0.8306 (mp0) REVERT: M 362 MET cc_start: 0.8226 (ptp) cc_final: 0.7860 (ptm) REVERT: G 10 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8421 (mm-30) REVERT: G 23 LYS cc_start: 0.9316 (tptm) cc_final: 0.8987 (tptp) REVERT: G 31 LYS cc_start: 0.8831 (tttm) cc_final: 0.8572 (tttm) REVERT: G 46 GLU cc_start: 0.8674 (tt0) cc_final: 0.8413 (tt0) REVERT: G 65 GLN cc_start: 0.8246 (tt0) cc_final: 0.7981 (mt0) REVERT: G 81 MET cc_start: 0.9334 (ttp) cc_final: 0.9089 (tmm) REVERT: G 82 GLU cc_start: 0.8699 (tt0) cc_final: 0.7971 (tm-30) REVERT: G 89 GLU cc_start: 0.9283 (pm20) cc_final: 0.9004 (pm20) REVERT: I 4 MET cc_start: 0.9169 (tpp) cc_final: 0.8688 (tpp) REVERT: I 42 GLN cc_start: 0.8344 (mt0) cc_final: 0.7968 (mp10) REVERT: I 70 GLN cc_start: 0.8860 (mt0) cc_final: 0.8449 (mm-40) REVERT: I 106 GLU cc_start: 0.8119 (tp30) cc_final: 0.7853 (tm-30) REVERT: N 113 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8059 (p0) REVERT: N 119 GLU cc_start: 0.9038 (mp0) cc_final: 0.8286 (mp0) REVERT: N 362 MET cc_start: 0.8227 (ptp) cc_final: 0.7865 (ptm) REVERT: H 10 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8426 (mm-30) REVERT: H 23 LYS cc_start: 0.9316 (tptm) cc_final: 0.8998 (tptp) REVERT: H 46 GLU cc_start: 0.8617 (tt0) cc_final: 0.8412 (tt0) REVERT: H 65 GLN cc_start: 0.8235 (tt0) cc_final: 0.7957 (mt0) REVERT: H 80 TYR cc_start: 0.8906 (m-10) cc_final: 0.8700 (m-10) REVERT: H 81 MET cc_start: 0.9330 (ttp) cc_final: 0.9075 (tmm) REVERT: H 82 GLU cc_start: 0.8687 (tt0) cc_final: 0.7960 (tm-30) REVERT: H 89 GLU cc_start: 0.9283 (pm20) cc_final: 0.9002 (pm20) REVERT: L 4 MET cc_start: 0.9194 (tpp) cc_final: 0.8836 (tpp) REVERT: L 42 GLN cc_start: 0.8376 (mt0) cc_final: 0.7992 (mp10) REVERT: L 70 GLN cc_start: 0.8809 (mm110) cc_final: 0.8470 (mm110) REVERT: L 101 GLN cc_start: 0.8045 (pm20) cc_final: 0.7775 (pm20) REVERT: L 104 LYS cc_start: 0.9073 (tptp) cc_final: 0.8797 (tptt) REVERT: O 113 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8025 (p0) REVERT: O 119 GLU cc_start: 0.9035 (mp0) cc_final: 0.8283 (mp0) REVERT: O 362 MET cc_start: 0.8235 (ptp) cc_final: 0.7870 (ptm) REVERT: J 10 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8428 (mm-30) REVERT: J 23 LYS cc_start: 0.9320 (tptm) cc_final: 0.8998 (tptp) REVERT: J 31 LYS cc_start: 0.8838 (tttm) cc_final: 0.8575 (tttm) REVERT: J 46 GLU cc_start: 0.8692 (tt0) cc_final: 0.8444 (tt0) REVERT: J 65 GLN cc_start: 0.8235 (tt0) cc_final: 0.7968 (mt0) REVERT: J 81 MET cc_start: 0.9331 (ttp) cc_final: 0.9077 (tmm) REVERT: J 82 GLU cc_start: 0.8686 (tt0) cc_final: 0.7960 (tm-30) REVERT: J 89 GLU cc_start: 0.9279 (pm20) cc_final: 0.8999 (pm20) REVERT: K 4 MET cc_start: 0.9206 (tpp) cc_final: 0.8730 (tpp) REVERT: K 42 GLN cc_start: 0.8367 (mt0) cc_final: 0.7984 (mp10) REVERT: K 70 GLN cc_start: 0.8809 (mm110) cc_final: 0.8407 (mm110) REVERT: P 113 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8044 (p0) REVERT: P 119 GLU cc_start: 0.9039 (mp0) cc_final: 0.8281 (mp0) REVERT: P 362 MET cc_start: 0.8230 (ptp) cc_final: 0.7867 (ptm) outliers start: 27 outliers final: 18 residues processed: 377 average time/residue: 0.3689 time to fit residues: 207.4674 Evaluate side-chains 355 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 333 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU 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 G residue 34 LEU 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 113 ASP Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 83 LEU 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 J residue 34 LEU 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 113 ASP Chi-restraints excluded: chain P residue 230 CYS 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 90 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 162 optimal weight: 0.0040 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049056 restraints weight = 61182.736| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.83 r_work: 0.2621 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21029 Z= 0.290 Angle : 0.724 8.116 28734 Z= 0.357 Chirality : 0.046 0.200 3354 Planarity : 0.004 0.036 3526 Dihedral : 7.593 51.970 4464 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % Rotamer: Outliers : 2.58 % Allowed : 11.84 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2477 helix: -1.43 (0.89), residues: 28 sheet: -0.30 (0.17), residues: 910 loop : -0.33 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 178 HIS 0.004 0.001 HIS O 347 PHE 0.015 0.002 PHE K 83 TYR 0.020 0.002 TYR J 80 ARG 0.006 0.001 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 24) link_NAG-ASN : angle 2.38870 ( 72) link_ALPHA1-6 : bond 0.00264 ( 10) link_ALPHA1-6 : angle 1.59787 ( 30) link_BETA1-4 : bond 0.00346 ( 40) link_BETA1-4 : angle 2.21995 ( 120) link_ALPHA1-2 : bond 0.00291 ( 4) link_ALPHA1-2 : angle 2.18834 ( 12) link_ALPHA1-3 : bond 0.00552 ( 8) link_ALPHA1-3 : angle 2.50037 ( 24) hydrogen bonds : bond 0.03777 ( 643) hydrogen bonds : angle 6.64064 ( 1632) SS BOND : bond 0.00391 ( 44) SS BOND : angle 0.46463 ( 88) covalent geometry : bond 0.00644 (20899) covalent geometry : angle 0.69619 (28388) *********************** 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 386 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 2.500 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: 0.8831 (mm-30) cc_final: 0.8620 (mm-30) REVERT: E 23 LYS cc_start: 0.9290 (tptm) cc_final: 0.8956 (tptp) REVERT: E 65 GLN cc_start: 0.8689 (tt0) cc_final: 0.8160 (mt0) REVERT: E 81 MET cc_start: 0.9452 (ttp) cc_final: 0.9060 (tmm) REVERT: E 82 GLU cc_start: 0.8747 (tt0) cc_final: 0.8035 (tm-30) REVERT: F 42 GLN cc_start: 0.8484 (mt0) cc_final: 0.7993 (mp10) REVERT: F 70 GLN cc_start: 0.8736 (mm110) cc_final: 0.8460 (mm110) REVERT: F 104 LYS cc_start: 0.9034 (tptp) cc_final: 0.8822 (tptp) REVERT: M 113 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8075 (p0) REVERT: M 119 GLU cc_start: 0.9063 (mp0) cc_final: 0.8305 (mp0) REVERT: M 362 MET cc_start: 0.8282 (ptp) cc_final: 0.7963 (ptm) REVERT: G 10 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8513 (mm-30) REVERT: G 23 LYS cc_start: 0.9303 (tptm) cc_final: 0.8943 (tptp) REVERT: G 46 GLU cc_start: 0.8683 (tt0) cc_final: 0.8358 (tt0) REVERT: G 65 GLN cc_start: 0.8369 (tt0) cc_final: 0.8099 (mt0) REVERT: G 81 MET cc_start: 0.9388 (ttp) cc_final: 0.9054 (tmm) REVERT: G 82 GLU cc_start: 0.8751 (tt0) cc_final: 0.8090 (tm-30) REVERT: G 89 GLU cc_start: 0.9323 (pm20) cc_final: 0.9117 (pm20) REVERT: I 42 GLN cc_start: 0.8449 (mt0) cc_final: 0.8019 (mp10) REVERT: I 70 GLN cc_start: 0.8892 (mt0) cc_final: 0.8501 (mm-40) REVERT: N 113 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8079 (p0) REVERT: N 119 GLU cc_start: 0.9081 (mp0) cc_final: 0.8315 (mp0) REVERT: N 362 MET cc_start: 0.8291 (ptp) cc_final: 0.7976 (ptm) REVERT: H 10 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8512 (mm-30) REVERT: H 23 LYS cc_start: 0.9292 (tptm) cc_final: 0.8961 (tptp) REVERT: H 65 GLN cc_start: 0.8368 (tt0) cc_final: 0.8076 (mt0) REVERT: H 81 MET cc_start: 0.9396 (ttp) cc_final: 0.9051 (tmm) REVERT: H 82 GLU cc_start: 0.8741 (tt0) cc_final: 0.8067 (tm-30) REVERT: H 89 GLU cc_start: 0.9320 (pm20) cc_final: 0.9114 (pm20) REVERT: L 42 GLN cc_start: 0.8478 (mt0) cc_final: 0.8020 (mp10) REVERT: L 70 GLN cc_start: 0.8751 (mm110) cc_final: 0.8416 (mm110) REVERT: L 101 GLN cc_start: 0.8156 (pm20) cc_final: 0.7859 (pm20) REVERT: L 104 LYS cc_start: 0.9063 (tptp) cc_final: 0.8570 (tptp) REVERT: O 113 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8066 (p0) REVERT: O 119 GLU cc_start: 0.9081 (mp0) cc_final: 0.8318 (mp0) REVERT: O 362 MET cc_start: 0.8296 (ptp) cc_final: 0.7977 (ptm) REVERT: J 10 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8473 (mm-30) REVERT: J 23 LYS cc_start: 0.9297 (tptm) cc_final: 0.8948 (tptp) REVERT: J 46 GLU cc_start: 0.8696 (tt0) cc_final: 0.8371 (tt0) REVERT: J 65 GLN cc_start: 0.8368 (tt0) cc_final: 0.8096 (mt0) REVERT: J 81 MET cc_start: 0.9394 (ttp) cc_final: 0.9052 (tmm) REVERT: J 82 GLU cc_start: 0.8734 (tt0) cc_final: 0.8077 (tm-30) REVERT: J 89 GLU cc_start: 0.9327 (pm20) cc_final: 0.9126 (pm20) REVERT: K 42 GLN cc_start: 0.8457 (mt0) cc_final: 0.8026 (mp10) REVERT: K 70 GLN cc_start: 0.8733 (mm110) cc_final: 0.8356 (mm110) REVERT: P 113 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8116 (p0) REVERT: P 119 GLU cc_start: 0.9059 (mp0) cc_final: 0.8307 (mp0) REVERT: P 362 MET cc_start: 0.8293 (ptp) cc_final: 0.7977 (ptm) outliers start: 55 outliers final: 37 residues processed: 362 average time/residue: 0.3506 time to fit residues: 194.6644 Evaluate side-chains 363 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 2.512 ------------------------------------------------------------------------------- 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 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 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 52 ILE 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 238 THR 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 34 LEU Chi-restraints excluded: chain H residue 52 ILE 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 238 THR 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 34 LEU Chi-restraints excluded: chain J residue 52 ILE 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 238 THR Chi-restraints excluded: chain P residue 443 ILE 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 128 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049570 restraints weight = 60032.481| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.78 r_work: 0.2677 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21029 Z= 0.150 Angle : 0.643 7.708 28734 Z= 0.321 Chirality : 0.044 0.207 3354 Planarity : 0.004 0.040 3526 Dihedral : 7.029 56.183 4464 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 2.72 % Allowed : 12.64 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2477 helix: -1.40 (0.84), residues: 28 sheet: -0.25 (0.17), residues: 918 loop : -0.15 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 178 HIS 0.003 0.001 HIS O 274 PHE 0.018 0.001 PHE L 83 TYR 0.017 0.001 TYR E 80 ARG 0.008 0.001 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 24) link_NAG-ASN : angle 1.91097 ( 72) link_ALPHA1-6 : bond 0.00562 ( 10) link_ALPHA1-6 : angle 1.39275 ( 30) link_BETA1-4 : bond 0.00415 ( 40) link_BETA1-4 : angle 1.74701 ( 120) link_ALPHA1-2 : bond 0.00662 ( 4) link_ALPHA1-2 : angle 2.33448 ( 12) link_ALPHA1-3 : bond 0.00964 ( 8) link_ALPHA1-3 : angle 1.78842 ( 24) hydrogen bonds : bond 0.03413 ( 643) hydrogen bonds : angle 6.45412 ( 1632) SS BOND : bond 0.00249 ( 44) SS BOND : angle 0.42524 ( 88) covalent geometry : bond 0.00331 (20899) covalent geometry : angle 0.62371 (28388) *********************** 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 413 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 355 time to evaluate : 2.560 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: 0.8862 (mm-30) cc_final: 0.8552 (mm-30) REVERT: E 23 LYS cc_start: 0.9295 (tptm) cc_final: 0.9050 (tptp) REVERT: E 65 GLN cc_start: 0.8752 (tt0) cc_final: 0.8250 (mt0) REVERT: E 81 MET cc_start: 0.9364 (ttp) cc_final: 0.9133 (tmm) REVERT: E 82 GLU cc_start: 0.8783 (tt0) cc_final: 0.8043 (tm-30) REVERT: F 4 MET cc_start: 0.9201 (tpp) cc_final: 0.8765 (tpp) REVERT: F 27 ARG cc_start: 0.9082 (ptt90) cc_final: 0.8685 (ptt180) REVERT: F 42 GLN cc_start: 0.8484 (mt0) cc_final: 0.7996 (mp10) REVERT: F 70 GLN cc_start: 0.8803 (mm110) cc_final: 0.8518 (mm110) REVERT: F 101 GLN cc_start: 0.8308 (pm20) cc_final: 0.7916 (pm20) REVERT: F 104 LYS cc_start: 0.9042 (tptp) cc_final: 0.8816 (tptp) REVERT: M 113 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8112 (p0) REVERT: M 119 GLU cc_start: 0.9022 (mp0) cc_final: 0.8275 (mp0) REVERT: M 362 MET cc_start: 0.8177 (ptp) cc_final: 0.7849 (ptm) REVERT: G 10 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8548 (mm-30) REVERT: G 23 LYS cc_start: 0.9324 (tptm) cc_final: 0.8956 (tptp) REVERT: G 46 GLU cc_start: 0.8700 (tt0) cc_final: 0.8365 (tt0) REVERT: G 65 GLN cc_start: 0.8311 (tt0) cc_final: 0.8091 (mt0) REVERT: G 81 MET cc_start: 0.9297 (ttp) cc_final: 0.8967 (tmm) REVERT: G 82 GLU cc_start: 0.8750 (tt0) cc_final: 0.8080 (tm-30) REVERT: G 89 GLU cc_start: 0.9367 (pm20) cc_final: 0.9130 (pm20) REVERT: I 4 MET cc_start: 0.9196 (tpp) cc_final: 0.8740 (tpp) REVERT: I 27 ARG cc_start: 0.9076 (ptt90) cc_final: 0.8665 (ptt180) REVERT: I 42 GLN cc_start: 0.8416 (mt0) cc_final: 0.8011 (mp10) REVERT: I 70 GLN cc_start: 0.8960 (mt0) cc_final: 0.8593 (mm110) REVERT: I 101 GLN cc_start: 0.8311 (pm20) cc_final: 0.7915 (pm20) REVERT: N 113 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8164 (p0) REVERT: N 119 GLU cc_start: 0.9034 (mp0) cc_final: 0.8281 (mp0) REVERT: N 362 MET cc_start: 0.8196 (ptp) cc_final: 0.7872 (ptm) REVERT: H 10 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8543 (mm-30) REVERT: H 23 LYS cc_start: 0.9329 (tptm) cc_final: 0.9070 (tptp) REVERT: H 65 GLN cc_start: 0.8318 (tt0) cc_final: 0.8021 (mt0) REVERT: H 82 GLU cc_start: 0.8741 (tt0) cc_final: 0.8015 (tm-30) REVERT: H 89 GLU cc_start: 0.9362 (pm20) cc_final: 0.9126 (pm20) REVERT: L 4 MET cc_start: 0.9216 (tpp) cc_final: 0.8798 (tpp) REVERT: L 42 GLN cc_start: 0.8456 (mt0) cc_final: 0.8040 (mp10) REVERT: L 70 GLN cc_start: 0.8860 (mm110) cc_final: 0.8607 (mm110) REVERT: L 101 GLN cc_start: 0.8161 (pm20) cc_final: 0.7873 (pm20) REVERT: O 113 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8143 (p0) REVERT: O 119 GLU cc_start: 0.9046 (mp0) cc_final: 0.8297 (mp0) REVERT: O 362 MET cc_start: 0.8195 (ptp) cc_final: 0.7869 (ptm) REVERT: J 10 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8538 (mm-30) REVERT: J 23 LYS cc_start: 0.9343 (tptm) cc_final: 0.8997 (tptp) REVERT: J 46 GLU cc_start: 0.8717 (tt0) cc_final: 0.8385 (tt0) REVERT: J 65 GLN cc_start: 0.8309 (tt0) cc_final: 0.8085 (mt0) REVERT: J 81 MET cc_start: 0.9324 (ttp) cc_final: 0.8993 (tmm) REVERT: J 82 GLU cc_start: 0.8751 (tt0) cc_final: 0.8075 (tm-30) REVERT: J 89 GLU cc_start: 0.9368 (pm20) cc_final: 0.9137 (pm20) REVERT: K 4 MET cc_start: 0.9199 (tpp) cc_final: 0.8726 (tpp) REVERT: K 27 ARG cc_start: 0.9060 (ptt90) cc_final: 0.8652 (ptt180) REVERT: K 42 GLN cc_start: 0.8424 (mt0) cc_final: 0.8040 (mp10) REVERT: K 70 GLN cc_start: 0.8869 (mm110) cc_final: 0.8583 (mm110) REVERT: K 101 GLN cc_start: 0.8318 (pm20) cc_final: 0.7936 (pm20) REVERT: P 113 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8158 (p0) REVERT: P 119 GLU cc_start: 0.9015 (mp0) cc_final: 0.8275 (mp0) REVERT: P 362 MET cc_start: 0.8184 (ptp) cc_final: 0.7862 (ptm) outliers start: 58 outliers final: 38 residues processed: 382 average time/residue: 0.3496 time to fit residues: 202.5271 Evaluate side-chains 378 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 107 ILE 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 444 VAL Chi-restraints excluded: chain G residue 11 VAL 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 238 THR Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL 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 113 ASP Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 238 THR Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL 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 K residue 107 ILE Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 444 VAL 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 15 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 GLN J 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048208 restraints weight = 60810.152| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.79 r_work: 0.2639 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21029 Z= 0.248 Angle : 0.698 8.547 28734 Z= 0.345 Chirality : 0.045 0.214 3354 Planarity : 0.004 0.040 3526 Dihedral : 7.104 55.808 4464 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.80 % Rotamer: Outliers : 2.82 % Allowed : 13.81 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2477 helix: -0.92 (0.97), residues: 28 sheet: -0.29 (0.17), residues: 918 loop : -0.18 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 178 HIS 0.003 0.001 HIS M 347 PHE 0.017 0.002 PHE I 83 TYR 0.012 0.002 TYR M 121 ARG 0.009 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 24) link_NAG-ASN : angle 2.19836 ( 72) link_ALPHA1-6 : bond 0.00328 ( 10) link_ALPHA1-6 : angle 1.57387 ( 30) link_BETA1-4 : bond 0.00309 ( 40) link_BETA1-4 : angle 1.80756 ( 120) link_ALPHA1-2 : bond 0.00345 ( 4) link_ALPHA1-2 : angle 2.16855 ( 12) link_ALPHA1-3 : bond 0.00639 ( 8) link_ALPHA1-3 : angle 2.33545 ( 24) hydrogen bonds : bond 0.03619 ( 643) hydrogen bonds : angle 6.47787 ( 1632) SS BOND : bond 0.00332 ( 44) SS BOND : angle 0.41649 ( 88) covalent geometry : bond 0.00552 (20899) covalent geometry : angle 0.67593 (28388) *********************** 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 399 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 2.371 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: E 10 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 23 LYS cc_start: 0.9301 (tptm) cc_final: 0.8957 (tptp) REVERT: E 46 GLU cc_start: 0.8559 (tt0) cc_final: 0.8309 (tt0) REVERT: E 63 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9198 (ptpp) REVERT: E 65 GLN cc_start: 0.8836 (tt0) cc_final: 0.8210 (mt0) REVERT: E 81 MET cc_start: 0.9436 (ttp) cc_final: 0.9023 (tmm) REVERT: E 82 GLU cc_start: 0.8793 (tt0) cc_final: 0.8050 (tm-30) REVERT: E 89 GLU cc_start: 0.9409 (pm20) cc_final: 0.9072 (pm20) REVERT: F 4 MET cc_start: 0.9106 (tpp) cc_final: 0.8734 (tpp) REVERT: F 42 GLN cc_start: 0.8528 (mt0) cc_final: 0.8025 (mp10) REVERT: F 70 GLN cc_start: 0.8774 (mm110) cc_final: 0.8500 (mm110) REVERT: F 101 GLN cc_start: 0.8330 (pm20) cc_final: 0.7935 (pm20) REVERT: F 104 LYS cc_start: 0.9003 (tptp) cc_final: 0.8723 (tptp) REVERT: M 113 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8161 (p0) REVERT: M 119 GLU cc_start: 0.9033 (mp0) cc_final: 0.8377 (mp0) REVERT: M 362 MET cc_start: 0.8247 (ptp) cc_final: 0.7913 (ptm) REVERT: G 10 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8501 (mm-30) REVERT: G 23 LYS cc_start: 0.9339 (tptm) cc_final: 0.8966 (tptp) REVERT: G 46 GLU cc_start: 0.8724 (tt0) cc_final: 0.8331 (tt0) REVERT: G 65 GLN cc_start: 0.8362 (tt0) cc_final: 0.7728 (mt0) REVERT: G 81 MET cc_start: 0.9387 (ttp) cc_final: 0.8888 (tmm) REVERT: G 82 GLU cc_start: 0.8776 (tt0) cc_final: 0.8141 (tm-30) REVERT: G 89 GLU cc_start: 0.9393 (pm20) cc_final: 0.9135 (pm20) REVERT: I 4 MET cc_start: 0.9109 (tpp) cc_final: 0.8724 (tpp) REVERT: I 24 ARG cc_start: 0.8426 (mtp-110) cc_final: 0.8181 (mtp85) REVERT: I 42 GLN cc_start: 0.8459 (mt0) cc_final: 0.7990 (mp10) REVERT: I 101 GLN cc_start: 0.8363 (pm20) cc_final: 0.7972 (pm20) REVERT: N 113 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8188 (p0) REVERT: N 119 GLU cc_start: 0.9060 (mp0) cc_final: 0.8423 (mp0) REVERT: N 362 MET cc_start: 0.8270 (ptp) cc_final: 0.7940 (ptm) REVERT: H 10 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8525 (mm-30) REVERT: H 23 LYS cc_start: 0.9316 (tptm) cc_final: 0.8964 (tptp) REVERT: H 46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8296 (tt0) REVERT: H 63 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9191 (ptpp) REVERT: H 65 GLN cc_start: 0.8426 (tt0) cc_final: 0.7689 (mt0) REVERT: H 82 GLU cc_start: 0.8849 (tt0) cc_final: 0.7939 (tm-30) REVERT: H 89 GLU cc_start: 0.9389 (pm20) cc_final: 0.9129 (pm20) REVERT: L 42 GLN cc_start: 0.8500 (mt0) cc_final: 0.8048 (mp10) REVERT: L 70 GLN cc_start: 0.8867 (mm110) cc_final: 0.8573 (mm110) REVERT: L 101 GLN cc_start: 0.8201 (pm20) cc_final: 0.7905 (pm20) REVERT: L 104 LYS cc_start: 0.8969 (tptp) cc_final: 0.8242 (tptt) REVERT: O 113 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8151 (p0) REVERT: O 119 GLU cc_start: 0.9061 (mp0) cc_final: 0.8428 (mp0) REVERT: O 362 MET cc_start: 0.8270 (ptp) cc_final: 0.7939 (ptm) REVERT: J 10 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8510 (mm-30) REVERT: J 23 LYS cc_start: 0.9340 (tptm) cc_final: 0.8973 (tptp) REVERT: J 46 GLU cc_start: 0.8744 (tt0) cc_final: 0.8361 (tt0) REVERT: J 65 GLN cc_start: 0.8361 (tt0) cc_final: 0.7734 (mt0) REVERT: J 81 MET cc_start: 0.9403 (ttp) cc_final: 0.9036 (tmm) REVERT: J 82 GLU cc_start: 0.8761 (tt0) cc_final: 0.8073 (tm-30) REVERT: J 89 GLU cc_start: 0.9391 (pm20) cc_final: 0.9137 (pm20) REVERT: K 42 GLN cc_start: 0.8489 (mt0) cc_final: 0.8089 (mp10) REVERT: K 70 GLN cc_start: 0.8865 (mm110) cc_final: 0.8557 (mm110) REVERT: K 101 GLN cc_start: 0.8339 (pm20) cc_final: 0.7924 (pm20) REVERT: P 113 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8186 (p0) REVERT: P 119 GLU cc_start: 0.9050 (mp0) cc_final: 0.8419 (mp0) REVERT: P 362 MET cc_start: 0.8274 (ptp) cc_final: 0.7955 (ptm) outliers start: 60 outliers final: 48 residues processed: 375 average time/residue: 0.3727 time to fit residues: 212.6392 Evaluate side-chains 375 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 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 34 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 63 LYS 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 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 238 THR 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 34 LEU Chi-restraints excluded: chain H residue 52 ILE 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 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 238 THR 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 34 LEU Chi-restraints excluded: chain J residue 63 LYS 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 K residue 107 ILE Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 238 THR 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 200 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049334 restraints weight = 60494.510| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.77 r_work: 0.2671 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21029 Z= 0.184 Angle : 0.674 8.245 28734 Z= 0.335 Chirality : 0.045 0.214 3354 Planarity : 0.004 0.044 3526 Dihedral : 6.972 57.071 4464 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 2.91 % Allowed : 13.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2477 helix: -0.88 (0.94), residues: 28 sheet: -0.19 (0.16), residues: 958 loop : -0.16 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 178 HIS 0.003 0.001 HIS O 274 PHE 0.034 0.002 PHE K 83 TYR 0.012 0.001 TYR M 121 ARG 0.009 0.001 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 24) link_NAG-ASN : angle 1.94896 ( 72) link_ALPHA1-6 : bond 0.00469 ( 10) link_ALPHA1-6 : angle 1.46655 ( 30) link_BETA1-4 : bond 0.00362 ( 40) link_BETA1-4 : angle 1.58376 ( 120) link_ALPHA1-2 : bond 0.00521 ( 4) link_ALPHA1-2 : angle 2.31313 ( 12) link_ALPHA1-3 : bond 0.00841 ( 8) link_ALPHA1-3 : angle 1.96197 ( 24) hydrogen bonds : bond 0.03517 ( 643) hydrogen bonds : angle 6.41399 ( 1632) SS BOND : bond 0.00270 ( 44) SS BOND : angle 0.40240 ( 88) covalent geometry : bond 0.00412 (20899) covalent geometry : angle 0.65633 (28388) *********************** 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 390 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 2.199 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: 0.8875 (mm-30) cc_final: 0.8586 (mm-30) REVERT: E 23 LYS cc_start: 0.9304 (tptm) cc_final: 0.8951 (tptp) REVERT: E 46 GLU cc_start: 0.8521 (tt0) cc_final: 0.8303 (tt0) REVERT: E 63 LYS cc_start: 0.9467 (ptpp) cc_final: 0.9214 (ptpp) REVERT: E 65 GLN cc_start: 0.8845 (tt0) cc_final: 0.8225 (mt0) REVERT: E 81 MET cc_start: 0.9382 (ttp) cc_final: 0.9118 (tmm) REVERT: E 82 GLU cc_start: 0.8807 (tt0) cc_final: 0.8071 (tm-30) REVERT: F 4 MET cc_start: 0.9126 (tpp) cc_final: 0.8798 (tpp) REVERT: F 27 ARG cc_start: 0.9080 (ptt90) cc_final: 0.8683 (ptt180) REVERT: F 42 GLN cc_start: 0.8510 (mt0) cc_final: 0.8030 (mp10) REVERT: F 70 GLN cc_start: 0.8769 (mm110) cc_final: 0.8513 (mm110) REVERT: F 101 GLN cc_start: 0.8336 (pm20) cc_final: 0.7927 (pm20) REVERT: F 104 LYS cc_start: 0.8976 (tptp) cc_final: 0.8749 (tptp) REVERT: M 113 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8210 (p0) REVERT: M 119 GLU cc_start: 0.9035 (mp0) cc_final: 0.8397 (mp0) REVERT: M 362 MET cc_start: 0.8188 (ptp) cc_final: 0.7860 (ptm) REVERT: G 10 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8594 (mm-30) REVERT: G 23 LYS cc_start: 0.9327 (tptm) cc_final: 0.8959 (tptp) REVERT: G 46 GLU cc_start: 0.8707 (tt0) cc_final: 0.8352 (tt0) REVERT: G 65 GLN cc_start: 0.8372 (tt0) cc_final: 0.8078 (mt0) REVERT: G 81 MET cc_start: 0.9367 (ttp) cc_final: 0.8946 (tmm) REVERT: G 82 GLU cc_start: 0.8776 (tt0) cc_final: 0.8162 (tm-30) REVERT: G 89 GLU cc_start: 0.9414 (pm20) cc_final: 0.9147 (pm20) REVERT: I 4 MET cc_start: 0.9122 (tpp) cc_final: 0.8769 (tpp) REVERT: I 27 ARG cc_start: 0.9097 (ptt90) cc_final: 0.8691 (ptt180) REVERT: I 42 GLN cc_start: 0.8466 (mt0) cc_final: 0.7999 (mp10) REVERT: I 70 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8533 (mm110) REVERT: I 101 GLN cc_start: 0.8319 (pm20) cc_final: 0.7915 (pm20) REVERT: N 113 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8225 (p0) REVERT: N 119 GLU cc_start: 0.9039 (mp0) cc_final: 0.8395 (mp0) REVERT: N 362 MET cc_start: 0.8208 (ptp) cc_final: 0.7868 (ptm) REVERT: H 10 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8598 (mm-30) REVERT: H 23 LYS cc_start: 0.9321 (tptm) cc_final: 0.8955 (tptp) REVERT: H 46 GLU cc_start: 0.8516 (tt0) cc_final: 0.8218 (tt0) REVERT: H 63 LYS cc_start: 0.9465 (ptpp) cc_final: 0.9173 (ptpp) REVERT: H 65 GLN cc_start: 0.8416 (tt0) cc_final: 0.7699 (mt0) REVERT: H 82 GLU cc_start: 0.8856 (tt0) cc_final: 0.7953 (tm-30) REVERT: H 89 GLU cc_start: 0.9410 (pm20) cc_final: 0.9143 (pm20) REVERT: L 4 MET cc_start: 0.9181 (tpp) cc_final: 0.8772 (tpp) REVERT: L 42 GLN cc_start: 0.8486 (mt0) cc_final: 0.8050 (mp10) REVERT: L 70 GLN cc_start: 0.8877 (mm110) cc_final: 0.8605 (mm110) REVERT: L 101 GLN cc_start: 0.8190 (pm20) cc_final: 0.7874 (pm20) REVERT: O 113 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8205 (p0) REVERT: O 362 MET cc_start: 0.8207 (ptp) cc_final: 0.7862 (ptm) REVERT: J 10 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8538 (mm-30) REVERT: J 23 LYS cc_start: 0.9343 (tptm) cc_final: 0.8979 (tptp) REVERT: J 46 GLU cc_start: 0.8714 (tt0) cc_final: 0.8358 (tt0) REVERT: J 65 GLN cc_start: 0.8362 (tt0) cc_final: 0.8074 (mt0) REVERT: J 81 MET cc_start: 0.9367 (ttp) cc_final: 0.8982 (tmm) REVERT: J 82 GLU cc_start: 0.8765 (tt0) cc_final: 0.8140 (tm-30) REVERT: J 89 GLU cc_start: 0.9398 (pm20) cc_final: 0.9159 (pm20) REVERT: K 4 MET cc_start: 0.9163 (tpp) cc_final: 0.8723 (tpp) REVERT: K 42 GLN cc_start: 0.8468 (mt0) cc_final: 0.8038 (mp10) REVERT: K 70 GLN cc_start: 0.8862 (mm110) cc_final: 0.8554 (mm110) REVERT: K 101 GLN cc_start: 0.8308 (pm20) cc_final: 0.7903 (pm20) REVERT: P 113 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8210 (p0) REVERT: P 119 GLU cc_start: 0.9040 (mp0) cc_final: 0.8407 (mp0) REVERT: P 362 MET cc_start: 0.8219 (ptp) cc_final: 0.7890 (ptm) outliers start: 62 outliers final: 49 residues processed: 371 average time/residue: 0.3239 time to fit residues: 181.5894 Evaluate side-chains 373 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 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 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 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 140 LEU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 238 THR 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 34 LEU 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 140 LEU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 238 THR 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 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 K residue 107 ILE Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 238 THR 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 130 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.063603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049111 restraints weight = 61043.932| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.81 r_work: 0.2665 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21029 Z= 0.199 Angle : 0.688 7.420 28734 Z= 0.343 Chirality : 0.045 0.217 3354 Planarity : 0.004 0.050 3526 Dihedral : 6.966 57.810 4464 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.68 % Allowed : 14.04 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2477 helix: -0.69 (0.99), residues: 28 sheet: -0.13 (0.17), residues: 892 loop : -0.13 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 178 HIS 0.003 0.001 HIS O 274 PHE 0.031 0.002 PHE K 83 TYR 0.011 0.001 TYR M 121 ARG 0.010 0.001 ARG J 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 24) link_NAG-ASN : angle 1.97352 ( 72) link_ALPHA1-6 : bond 0.00425 ( 10) link_ALPHA1-6 : angle 1.50569 ( 30) link_BETA1-4 : bond 0.00332 ( 40) link_BETA1-4 : angle 1.56308 ( 120) link_ALPHA1-2 : bond 0.00465 ( 4) link_ALPHA1-2 : angle 2.20623 ( 12) link_ALPHA1-3 : bond 0.00785 ( 8) link_ALPHA1-3 : angle 2.06127 ( 24) hydrogen bonds : bond 0.03533 ( 643) hydrogen bonds : angle 6.40138 ( 1632) SS BOND : bond 0.00275 ( 44) SS BOND : angle 0.39054 ( 88) covalent geometry : bond 0.00448 (20899) covalent geometry : angle 0.67107 (28388) *********************** 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 376 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 2.450 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: 0.8870 (mm-30) cc_final: 0.8584 (mm-30) REVERT: E 23 LYS cc_start: 0.9302 (tptm) cc_final: 0.8928 (tptp) REVERT: E 46 GLU cc_start: 0.8522 (tt0) cc_final: 0.8237 (tt0) REVERT: E 63 LYS cc_start: 0.9460 (ptpp) cc_final: 0.9201 (ptpp) REVERT: E 65 GLN cc_start: 0.8872 (tt0) cc_final: 0.8263 (mt0) REVERT: E 81 MET cc_start: 0.9434 (ttp) cc_final: 0.9101 (tmm) REVERT: E 82 GLU cc_start: 0.8813 (tt0) cc_final: 0.8154 (tm-30) REVERT: F 27 ARG cc_start: 0.9081 (ptt90) cc_final: 0.8677 (ptt180) REVERT: F 42 GLN cc_start: 0.8528 (mt0) cc_final: 0.8080 (mp10) REVERT: F 70 GLN cc_start: 0.8771 (mm110) cc_final: 0.8474 (mm110) REVERT: F 101 GLN cc_start: 0.8339 (pm20) cc_final: 0.7917 (pm20) REVERT: F 104 LYS cc_start: 0.8928 (tptp) cc_final: 0.8193 (tptp) REVERT: M 113 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8189 (p0) REVERT: M 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.8402 (mp0) REVERT: M 198 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8723 (m-30) REVERT: M 362 MET cc_start: 0.8201 (ptp) cc_final: 0.7863 (ptm) REVERT: G 10 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8601 (mm-30) REVERT: G 23 LYS cc_start: 0.9326 (tptm) cc_final: 0.8953 (tptp) REVERT: G 46 GLU cc_start: 0.8802 (tt0) cc_final: 0.8469 (tt0) REVERT: G 65 GLN cc_start: 0.8377 (tt0) cc_final: 0.7744 (mt0) REVERT: G 81 MET cc_start: 0.9373 (ttp) cc_final: 0.8920 (tmm) REVERT: G 82 GLU cc_start: 0.8796 (tt0) cc_final: 0.8191 (tm-30) REVERT: G 89 GLU cc_start: 0.9383 (pm20) cc_final: 0.9118 (pm20) REVERT: I 27 ARG cc_start: 0.9110 (ptt90) cc_final: 0.8711 (ptt180) REVERT: I 42 GLN cc_start: 0.8492 (mt0) cc_final: 0.8062 (mp10) REVERT: I 70 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8555 (mm110) REVERT: I 101 GLN cc_start: 0.8348 (pm20) cc_final: 0.7936 (pm20) REVERT: I 106 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7684 (mp0) REVERT: N 113 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8248 (p0) REVERT: N 119 GLU cc_start: 0.9036 (mp0) cc_final: 0.8405 (mp0) REVERT: N 362 MET cc_start: 0.8216 (ptp) cc_final: 0.7890 (ptm) REVERT: H 10 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8615 (mm-30) REVERT: H 23 LYS cc_start: 0.9328 (tptm) cc_final: 0.8967 (tptp) REVERT: H 46 GLU cc_start: 0.8532 (tt0) cc_final: 0.8272 (tt0) REVERT: H 63 LYS cc_start: 0.9469 (ptpp) cc_final: 0.9200 (ptpp) REVERT: H 65 GLN cc_start: 0.8452 (tt0) cc_final: 0.7729 (mt0) REVERT: H 82 GLU cc_start: 0.8868 (tt0) cc_final: 0.7998 (tm-30) REVERT: H 89 GLU cc_start: 0.9379 (pm20) cc_final: 0.9115 (pm20) REVERT: L 4 MET cc_start: 0.9183 (tpp) cc_final: 0.8796 (tpp) REVERT: L 42 GLN cc_start: 0.8489 (mt0) cc_final: 0.8060 (mp10) REVERT: L 70 GLN cc_start: 0.8881 (mm110) cc_final: 0.8613 (mm110) REVERT: L 101 GLN cc_start: 0.8235 (pm20) cc_final: 0.7897 (pm20) REVERT: O 113 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8235 (p0) REVERT: O 119 GLU cc_start: 0.9043 (mp0) cc_final: 0.8535 (mp0) REVERT: O 362 MET cc_start: 0.8221 (ptp) cc_final: 0.7890 (ptm) REVERT: J 10 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8553 (mm-30) REVERT: J 23 LYS cc_start: 0.9344 (tptm) cc_final: 0.8978 (tptp) REVERT: J 46 GLU cc_start: 0.8810 (tt0) cc_final: 0.8470 (tt0) REVERT: J 65 GLN cc_start: 0.8393 (tt0) cc_final: 0.7758 (mt0) REVERT: J 81 MET cc_start: 0.9412 (ttp) cc_final: 0.8953 (tmm) REVERT: J 82 GLU cc_start: 0.8789 (tt0) cc_final: 0.8232 (tm-30) REVERT: J 89 GLU cc_start: 0.9398 (pm20) cc_final: 0.9131 (pm20) REVERT: K 4 MET cc_start: 0.9181 (tpp) cc_final: 0.8754 (tpp) REVERT: K 42 GLN cc_start: 0.8506 (mt0) cc_final: 0.8080 (mp10) REVERT: K 70 GLN cc_start: 0.8870 (mm110) cc_final: 0.8569 (mm110) REVERT: K 101 GLN cc_start: 0.8326 (pm20) cc_final: 0.7918 (pm20) REVERT: P 113 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8225 (p0) REVERT: P 119 GLU cc_start: 0.9026 (mp0) cc_final: 0.8392 (mp0) REVERT: P 362 MET cc_start: 0.8229 (ptp) cc_final: 0.7906 (ptm) outliers start: 57 outliers final: 47 residues processed: 356 average time/residue: 0.3467 time to fit residues: 187.4115 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 : 2.348 ------------------------------------------------------------------------------- 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 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 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 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 140 LEU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 238 THR 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 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 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 238 THR 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 34 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 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 238 THR 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 76 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.050097 restraints weight = 60297.464| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.80 r_work: 0.2695 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21029 Z= 0.146 Angle : 0.679 7.660 28734 Z= 0.338 Chirality : 0.045 0.218 3354 Planarity : 0.004 0.047 3526 Dihedral : 6.778 59.274 4464 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 2.35 % Allowed : 14.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2477 helix: -0.71 (0.97), residues: 28 sheet: -0.19 (0.17), residues: 938 loop : -0.00 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 178 HIS 0.003 0.001 HIS O 274 PHE 0.028 0.001 PHE K 83 TYR 0.011 0.001 TYR M 121 ARG 0.011 0.001 ARG E 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 24) link_NAG-ASN : angle 1.76599 ( 72) link_ALPHA1-6 : bond 0.00552 ( 10) link_ALPHA1-6 : angle 1.43962 ( 30) link_BETA1-4 : bond 0.00386 ( 40) link_BETA1-4 : angle 1.45330 ( 120) link_ALPHA1-2 : bond 0.00611 ( 4) link_ALPHA1-2 : angle 2.23555 ( 12) link_ALPHA1-3 : bond 0.00965 ( 8) link_ALPHA1-3 : angle 1.78944 ( 24) hydrogen bonds : bond 0.03406 ( 643) hydrogen bonds : angle 6.29633 ( 1632) SS BOND : bond 0.00208 ( 44) SS BOND : angle 0.36862 ( 88) covalent geometry : bond 0.00333 (20899) covalent geometry : angle 0.66545 (28388) ********************** 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 384 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 2.221 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 3 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8511 (mm-40) REVERT: E 10 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8623 (mm-30) REVERT: E 19 ARG cc_start: 0.9361 (mmm-85) cc_final: 0.9036 (mmm160) REVERT: E 23 LYS cc_start: 0.9304 (tptm) cc_final: 0.8946 (tptp) REVERT: E 46 GLU cc_start: 0.8548 (tt0) cc_final: 0.8207 (tt0) REVERT: E 63 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9211 (ptpp) REVERT: E 65 GLN cc_start: 0.8871 (tt0) cc_final: 0.8237 (mt0) REVERT: E 81 MET cc_start: 0.9402 (ttp) cc_final: 0.8967 (tmm) REVERT: E 82 GLU cc_start: 0.8817 (tt0) cc_final: 0.8141 (tm-30) REVERT: F 4 MET cc_start: 0.9184 (tpp) cc_final: 0.8743 (tpp) REVERT: F 42 GLN cc_start: 0.8480 (mt0) cc_final: 0.8047 (mp10) REVERT: F 70 GLN cc_start: 0.8827 (mm110) cc_final: 0.8513 (mm110) REVERT: F 101 GLN cc_start: 0.8329 (pm20) cc_final: 0.7883 (pm20) REVERT: M 113 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8203 (p0) REVERT: M 119 GLU cc_start: 0.9002 (mp0) cc_final: 0.8348 (mp0) REVERT: M 198 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8730 (m-30) REVERT: M 362 MET cc_start: 0.8173 (ptp) cc_final: 0.7852 (ptm) REVERT: G 10 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8614 (mm-30) REVERT: G 19 ARG cc_start: 0.9368 (mmm-85) cc_final: 0.9145 (mmm-85) REVERT: G 23 LYS cc_start: 0.9336 (tptm) cc_final: 0.8973 (tptp) REVERT: G 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8480 (tt0) REVERT: G 65 GLN cc_start: 0.8406 (tt0) cc_final: 0.7831 (mt0) REVERT: G 81 MET cc_start: 0.9339 (ttp) cc_final: 0.8942 (tmm) REVERT: G 82 GLU cc_start: 0.8808 (tt0) cc_final: 0.8160 (tm-30) REVERT: G 89 GLU cc_start: 0.9363 (pm20) cc_final: 0.9077 (pm20) REVERT: I 4 MET cc_start: 0.9201 (tpp) cc_final: 0.8745 (tpp) REVERT: I 42 GLN cc_start: 0.8453 (mt0) cc_final: 0.8034 (mp10) REVERT: I 70 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8580 (mm110) REVERT: I 101 GLN cc_start: 0.8335 (pm20) cc_final: 0.7923 (pm20) REVERT: I 106 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: N 113 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8256 (p0) REVERT: N 119 GLU cc_start: 0.9013 (mp0) cc_final: 0.8361 (mp0) REVERT: N 362 MET cc_start: 0.8180 (ptp) cc_final: 0.7893 (ptm) REVERT: H 10 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8595 (mm-30) REVERT: H 19 ARG cc_start: 0.9361 (mmm-85) cc_final: 0.9145 (mmm-85) REVERT: H 23 LYS cc_start: 0.9332 (tptm) cc_final: 0.8973 (tptp) REVERT: H 46 GLU cc_start: 0.8555 (tt0) cc_final: 0.8231 (tt0) REVERT: H 63 LYS cc_start: 0.9463 (ptpp) cc_final: 0.9183 (ptpp) REVERT: H 65 GLN cc_start: 0.8461 (tt0) cc_final: 0.7770 (mt0) REVERT: H 82 GLU cc_start: 0.8890 (tt0) cc_final: 0.7923 (tm-30) REVERT: H 89 GLU cc_start: 0.9362 (pm20) cc_final: 0.9077 (pm20) REVERT: L 4 MET cc_start: 0.9188 (tpp) cc_final: 0.8773 (tpp) REVERT: L 42 GLN cc_start: 0.8447 (mt0) cc_final: 0.8037 (mp10) REVERT: L 70 GLN cc_start: 0.8886 (mm110) cc_final: 0.8605 (mm110) REVERT: L 101 GLN cc_start: 0.8207 (pm20) cc_final: 0.7879 (pm20) REVERT: L 108 LYS cc_start: 0.8696 (tppt) cc_final: 0.8138 (tppp) REVERT: O 113 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8239 (p0) REVERT: O 119 GLU cc_start: 0.9010 (mp0) cc_final: 0.8456 (mp0) REVERT: O 362 MET cc_start: 0.8182 (ptp) cc_final: 0.7889 (ptm) REVERT: J 10 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8554 (mm-30) REVERT: J 23 LYS cc_start: 0.9341 (tptm) cc_final: 0.8979 (tptp) REVERT: J 46 GLU cc_start: 0.8844 (tt0) cc_final: 0.8480 (tt0) REVERT: J 65 GLN cc_start: 0.8420 (tt0) cc_final: 0.7841 (mt0) REVERT: J 81 MET cc_start: 0.9397 (ttp) cc_final: 0.8961 (tmm) REVERT: J 82 GLU cc_start: 0.8772 (tt0) cc_final: 0.8205 (tm-30) REVERT: J 89 GLU cc_start: 0.9376 (pm20) cc_final: 0.9098 (pm20) REVERT: K 4 MET cc_start: 0.9220 (tpp) cc_final: 0.8773 (tpp) REVERT: K 42 GLN cc_start: 0.8442 (mt0) cc_final: 0.8045 (mp10) REVERT: K 70 GLN cc_start: 0.8858 (mm110) cc_final: 0.8598 (mm110) REVERT: K 101 GLN cc_start: 0.8338 (pm20) cc_final: 0.7906 (pm20) REVERT: K 108 LYS cc_start: 0.8715 (tppt) cc_final: 0.8238 (tppp) REVERT: P 113 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8235 (p0) REVERT: P 362 MET cc_start: 0.8195 (ptp) cc_final: 0.7909 (ptm) outliers start: 50 outliers final: 42 residues processed: 364 average time/residue: 0.3401 time to fit residues: 187.0017 Evaluate side-chains 369 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain F residue 46 LEU 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 34 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 I residue 106 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 238 THR 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 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 113 ASP Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 238 THR 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 34 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 238 THR 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 166 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049405 restraints weight = 61228.797| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.78 r_work: 0.2671 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21029 Z= 0.206 Angle : 0.692 7.490 28734 Z= 0.343 Chirality : 0.045 0.218 3354 Planarity : 0.004 0.058 3526 Dihedral : 6.833 58.726 4464 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 2.40 % Allowed : 15.41 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2477 helix: -0.48 (1.03), residues: 28 sheet: -0.22 (0.17), residues: 941 loop : -0.00 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 178 HIS 0.003 0.001 HIS O 274 PHE 0.024 0.002 PHE K 83 TYR 0.012 0.001 TYR O 121 ARG 0.011 0.001 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 24) link_NAG-ASN : angle 1.99955 ( 72) link_ALPHA1-6 : bond 0.00402 ( 10) link_ALPHA1-6 : angle 1.52572 ( 30) link_BETA1-4 : bond 0.00321 ( 40) link_BETA1-4 : angle 1.51831 ( 120) link_ALPHA1-2 : bond 0.00426 ( 4) link_ALPHA1-2 : angle 2.16884 ( 12) link_ALPHA1-3 : bond 0.00718 ( 8) link_ALPHA1-3 : angle 2.07426 ( 24) hydrogen bonds : bond 0.03540 ( 643) hydrogen bonds : angle 6.29851 ( 1632) SS BOND : bond 0.00288 ( 44) SS BOND : angle 0.38863 ( 88) covalent geometry : bond 0.00464 (20899) covalent geometry : angle 0.67590 (28388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10664.16 seconds wall clock time: 186 minutes 54.84 seconds (11214.84 seconds total)