Starting phenix.real_space_refine on Wed Nov 20 01:25:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_29686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_29686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_29686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_29686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/11_2024/8g30_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-5513/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: 12.31, per 1000 atoms: 0.60 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: 7.03 Conformation dependent library (CDL) restraints added in 2.7 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: 2.94 Creating SS restraints... Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.828A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.553A pdb=" N ALA M 110 " --> pdb=" O ILE M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.629A pdb=" N SER M 145 " --> pdb=" O ASN M 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN M 146 " --> pdb=" O VAL M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 142 through 146' Processing helix chain 'M' and resid 197 through 200 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER N 145 " --> pdb=" O ASN N 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN N 146 " --> pdb=" O VAL N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 142 through 146' Processing helix chain 'N' and resid 197 through 200 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.787A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 110 removed outlier: 3.551A pdb=" N ALA O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.584A pdb=" N SER O 145 " --> pdb=" O ASN O 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN O 146 " --> pdb=" O VAL O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 146' Processing helix chain 'O' and resid 197 through 200 Processing helix chain 'J' and resid 27 through 31 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA P 110 " --> pdb=" O ILE P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER P 145 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN P 146 " --> pdb=" O VAL P 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 197 through 200 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.414A pdb=" N LEU E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.868A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 33 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 97 through 102 removed outlier: 5.336A pdb=" N CYS M 447 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG M 420 " --> pdb=" O GLY M 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP M 115 " --> pdb=" O THR M 138 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR M 138 " --> pdb=" O TRP M 115 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR M 117 " --> pdb=" O GLN M 136 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN M 136 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU M 119 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU M 134 " --> pdb=" O GLU M 119 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU M 158 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS M 172 " --> pdb=" O MET M 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 179 through 184 removed outlier: 3.537A pdb=" N SER M 179 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR M 207 " --> pdb=" O LEU M 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU M 211 " --> pdb=" O TYR M 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 224 through 225 removed outlier: 3.501A pdb=" N VAL M 231 " --> pdb=" O THR M 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU M 258 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 276 through 283 removed outlier: 5.416A pdb=" N GLU M 277 " --> pdb=" O ARG M 292 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG M 292 " --> pdb=" O GLU M 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 352 through 356 removed outlier: 4.441A pdb=" N TRP M 352 " --> pdb=" O GLY M 363 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 363 " --> pdb=" O TRP M 352 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU M 372 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL M 398 " --> pdb=" O LEU M 372 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR M 374 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL M 396 " --> pdb=" O TYR M 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR M 376 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG M 394 " --> pdb=" O THR M 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.412A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.870A pdb=" N GLN I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 102 removed outlier: 5.347A pdb=" N CYS N 447 " --> pdb=" O PRO N 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG N 420 " --> pdb=" O GLY N 448 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP N 115 " --> pdb=" O THR N 138 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR N 138 " --> pdb=" O TRP N 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR N 117 " --> pdb=" O GLN N 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN N 136 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU N 119 " --> pdb=" O LEU N 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU N 134 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU N 158 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 172 " --> pdb=" O MET N 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 179 through 184 removed outlier: 3.551A pdb=" N SER N 179 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR N 207 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU N 211 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 224 through 225 Processing sheet with id=AC4, first strand: chain 'N' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU N 258 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU N 277 " --> pdb=" O ARG N 292 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG N 292 " --> pdb=" O GLU N 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 352 through 356 removed outlier: 4.442A pdb=" N TRP N 352 " --> pdb=" O GLY N 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY N 363 " --> pdb=" O TRP N 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU N 372 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL N 398 " --> pdb=" O LEU N 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR N 374 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL N 396 " --> pdb=" O TYR N 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR N 376 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 394 " --> pdb=" O THR N 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.411A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.866A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS O 447 " --> pdb=" O PRO O 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG O 420 " --> pdb=" O GLY O 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP O 115 " --> pdb=" O THR O 138 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR O 138 " --> pdb=" O TRP O 115 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR O 117 " --> pdb=" O GLN O 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN O 136 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU O 119 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU O 134 " --> pdb=" O GLU O 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU O 158 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS O 172 " --> pdb=" O MET O 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER O 179 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR O 207 " --> pdb=" O LEU O 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU O 211 " --> pdb=" O TYR O 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 224 through 225 Processing sheet with id=AD7, first strand: chain 'O' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU O 258 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE O 262 " --> pdb=" O GLU O 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 276 through 283 removed outlier: 5.427A pdb=" N GLU O 277 " --> pdb=" O ARG O 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG O 292 " --> pdb=" O GLU O 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 352 through 356 removed outlier: 4.443A pdb=" N TRP O 352 " --> pdb=" O GLY O 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY O 363 " --> pdb=" O TRP O 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU O 372 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL O 398 " --> pdb=" O LEU O 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR O 374 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL O 396 " --> pdb=" O TYR O 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR O 376 " --> pdb=" O ARG O 394 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG O 394 " --> pdb=" O THR O 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.414A pdb=" N LEU J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AE4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.865A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU K 33 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS P 447 " --> pdb=" O PRO P 99 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG P 420 " --> pdb=" O GLY P 448 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP P 115 " --> pdb=" O THR P 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR P 138 " --> pdb=" O TRP P 115 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR P 117 " --> pdb=" O GLN P 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN P 136 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU P 119 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU P 134 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU P 158 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS P 172 " --> pdb=" O MET P 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER P 179 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR P 207 " --> pdb=" O LEU P 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU P 211 " --> pdb=" O TYR P 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 224 through 225 Processing sheet with id=AF1, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU P 258 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE P 262 " --> pdb=" O GLU P 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU P 277 " --> pdb=" O ARG P 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG P 292 " --> pdb=" O GLU P 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 352 through 356 removed outlier: 4.439A pdb=" N TRP P 352 " --> pdb=" O GLY P 363 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY P 363 " --> pdb=" O TRP P 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU P 372 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL P 398 " --> pdb=" O LEU P 372 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR P 374 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL P 396 " --> pdb=" O TYR P 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR P 376 " --> pdb=" O ARG P 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG P 394 " --> pdb=" O THR P 376 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 7.22 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.880 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.160 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- 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 20899 Z= 1.035 Angle : 1.867 48.443 28388 Z= 1.223 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 *********************** 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 : 2.364 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: 0.3945 time to fit residues: 260.7982 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 : 2.167 ------------------------------------------------------------------------------- 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: 4.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** P 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20899 Z= 0.289 Angle : 0.767 7.181 28388 Z= 0.399 Chirality : 0.049 0.178 3354 Planarity : 0.004 0.036 3526 Dihedral : 13.070 78.882 4472 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 0.80 % Allowed : 10.38 % Favored : 88.82 % 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: -0.84 (0.17), residues: 2477 helix: -2.32 (0.77), residues: 28 sheet: -0.14 (0.18), residues: 886 loop : -0.76 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 115 HIS 0.002 0.001 HIS M 168 PHE 0.016 0.002 PHE I 83 TYR 0.017 0.002 TYR P 121 ARG 0.006 0.001 ARG G 106 *********************** 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 399 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 382 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 LYS cc_start: 0.9280 (tttp) cc_final: 0.8987 (tttm) REVERT: E 65 GLN cc_start: 0.8918 (tt0) cc_final: 0.8476 (mt0) REVERT: E 81 MET cc_start: 0.9566 (ttp) cc_final: 0.8976 (tmm) REVERT: E 82 GLU cc_start: 0.9234 (tt0) cc_final: 0.8710 (tm-30) REVERT: F 11 LEU cc_start: 0.9424 (tp) cc_final: 0.9161 (tp) REVERT: F 42 GLN cc_start: 0.8624 (mt0) cc_final: 0.8268 (mp10) REVERT: F 54 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8369 (mtm-85) REVERT: F 70 GLN cc_start: 0.9358 (mm110) cc_final: 0.9140 (mm110) REVERT: F 79 GLN cc_start: 0.9331 (mm110) cc_final: 0.9100 (mp10) REVERT: F 83 PHE cc_start: 0.8572 (m-80) cc_final: 0.8278 (m-80) REVERT: F 89 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8920 (tt0) REVERT: F 104 LYS cc_start: 0.9325 (tppt) cc_final: 0.8788 (tptt) REVERT: M 119 GLU cc_start: 0.9529 (mp0) cc_final: 0.9166 (mp0) REVERT: G 65 GLN cc_start: 0.8756 (tt0) cc_final: 0.8377 (mt0) REVERT: G 81 MET cc_start: 0.9554 (ttp) cc_final: 0.8989 (tmm) REVERT: G 82 GLU cc_start: 0.9249 (tt0) cc_final: 0.8735 (tm-30) REVERT: I 42 GLN cc_start: 0.8663 (mt0) cc_final: 0.8309 (mp10) REVERT: I 54 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8381 (mtm-85) REVERT: I 70 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9046 (mm-40) REVERT: I 79 GLN cc_start: 0.9326 (mm110) cc_final: 0.9020 (mm110) REVERT: I 89 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8920 (tt0) REVERT: N 119 GLU cc_start: 0.9561 (mp0) cc_final: 0.9326 (mp0) REVERT: H 65 GLN cc_start: 0.8762 (tt0) cc_final: 0.8379 (mt0) REVERT: H 81 MET cc_start: 0.9554 (ttp) cc_final: 0.8988 (tmm) REVERT: H 82 GLU cc_start: 0.9245 (tt0) cc_final: 0.8728 (tm-30) REVERT: L 42 GLN cc_start: 0.8662 (mt0) cc_final: 0.8306 (mp10) REVERT: L 54 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8374 (mtm-85) REVERT: L 79 GLN cc_start: 0.9314 (mm110) cc_final: 0.9007 (mm110) REVERT: L 89 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8926 (tt0) REVERT: O 119 GLU cc_start: 0.9563 (mp0) cc_final: 0.9330 (mp0) REVERT: J 65 GLN cc_start: 0.8753 (tt0) cc_final: 0.8376 (mt0) REVERT: J 81 MET cc_start: 0.9553 (ttp) cc_final: 0.8985 (tmm) REVERT: J 82 GLU cc_start: 0.9246 (tt0) cc_final: 0.8731 (tm-30) REVERT: K 42 GLN cc_start: 0.8651 (mt0) cc_final: 0.8300 (mp10) REVERT: K 54 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8376 (mtm-85) REVERT: K 89 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8912 (tt0) REVERT: K 106 GLU cc_start: 0.8594 (tp30) cc_final: 0.8319 (tm-30) REVERT: P 119 GLU cc_start: 0.9561 (mp0) cc_final: 0.9149 (mp0) outliers start: 17 outliers final: 15 residues processed: 389 average time/residue: 0.3973 time to fit residues: 226.2102 Evaluate side-chains 348 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 123 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20899 Z= 0.287 Angle : 0.707 7.939 28388 Z= 0.356 Chirality : 0.047 0.161 3354 Planarity : 0.004 0.049 3526 Dihedral : 9.837 59.693 4464 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.39 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 11.98 % Favored : 86.19 % 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: -0.60 (0.17), residues: 2477 helix: -1.70 (0.89), residues: 28 sheet: -0.28 (0.17), residues: 926 loop : -0.38 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 115 HIS 0.003 0.001 HIS O 274 PHE 0.020 0.002 PHE K 83 TYR 0.018 0.002 TYR M 121 ARG 0.007 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 2.340 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: E 65 GLN cc_start: 0.9100 (tt0) cc_final: 0.8624 (mt0) REVERT: E 81 MET cc_start: 0.9548 (ttp) cc_final: 0.9098 (tmm) REVERT: E 82 GLU cc_start: 0.9291 (tt0) cc_final: 0.8761 (tm-30) REVERT: F 42 GLN cc_start: 0.8717 (mt0) cc_final: 0.8282 (mp10) REVERT: F 83 PHE cc_start: 0.8639 (m-80) cc_final: 0.8376 (m-80) REVERT: M 119 GLU cc_start: 0.9551 (mp0) cc_final: 0.9244 (mp0) REVERT: M 362 MET cc_start: 0.8705 (ptp) cc_final: 0.8431 (ptm) REVERT: G 10 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8589 (mm-30) REVERT: G 65 GLN cc_start: 0.8875 (tt0) cc_final: 0.8494 (mt0) REVERT: G 81 MET cc_start: 0.9534 (ttp) cc_final: 0.9331 (tmm) REVERT: G 82 GLU cc_start: 0.9270 (tt0) cc_final: 0.8685 (tm-30) REVERT: I 4 MET cc_start: 0.9263 (tpp) cc_final: 0.8915 (tpp) REVERT: I 42 GLN cc_start: 0.8699 (mt0) cc_final: 0.8260 (mp10) REVERT: I 70 GLN cc_start: 0.9279 (mt0) cc_final: 0.9047 (mm-40) REVERT: N 119 GLU cc_start: 0.9544 (mp0) cc_final: 0.9140 (mp0) REVERT: N 362 MET cc_start: 0.8696 (ptp) cc_final: 0.8425 (ptm) REVERT: H 10 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8568 (mm-30) REVERT: H 65 GLN cc_start: 0.8885 (tt0) cc_final: 0.8501 (mt0) REVERT: H 81 MET cc_start: 0.9533 (ttp) cc_final: 0.9329 (tmm) REVERT: H 82 GLU cc_start: 0.9267 (tt0) cc_final: 0.8678 (tm-30) REVERT: L 42 GLN cc_start: 0.8697 (mt0) cc_final: 0.8259 (mp10) REVERT: O 119 GLU cc_start: 0.9550 (mp0) cc_final: 0.9150 (mp0) REVERT: O 362 MET cc_start: 0.8707 (ptp) cc_final: 0.8412 (ptm) REVERT: J 10 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8570 (mm-30) REVERT: J 65 GLN cc_start: 0.8869 (tt0) cc_final: 0.8491 (mt0) REVERT: J 81 MET cc_start: 0.9531 (ttp) cc_final: 0.9325 (tmm) REVERT: J 82 GLU cc_start: 0.9269 (tt0) cc_final: 0.8682 (tm-30) REVERT: K 42 GLN cc_start: 0.8693 (mt0) cc_final: 0.8257 (mp10) REVERT: K 54 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8492 (mtm-85) REVERT: P 119 GLU cc_start: 0.9550 (mp0) cc_final: 0.9148 (mp0) REVERT: P 362 MET cc_start: 0.8703 (ptp) cc_final: 0.8408 (ptm) outliers start: 39 outliers final: 38 residues processed: 364 average time/residue: 0.3657 time to fit residues: 199.5141 Evaluate side-chains 368 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 F residue 46 LEU Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 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 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 L residue 90 HIS Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 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 46 LEU Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN M 274 HIS N 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20899 Z= 0.348 Angle : 0.695 7.940 28388 Z= 0.351 Chirality : 0.046 0.187 3354 Planarity : 0.004 0.068 3526 Dihedral : 8.106 53.326 4464 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 1.97 % Allowed : 11.70 % Favored : 86.33 % 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: -0.61 (0.17), residues: 2477 helix: -1.46 (0.94), residues: 28 sheet: -0.33 (0.17), residues: 913 loop : -0.35 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 115 HIS 0.003 0.001 HIS M 191 PHE 0.015 0.002 PHE I 83 TYR 0.014 0.002 TYR O 121 ARG 0.008 0.001 ARG J 87 *********************** 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 383 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 2.605 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: 0.9136 (mm-30) cc_final: 0.8910 (mm-30) REVERT: E 65 GLN cc_start: 0.9205 (tt0) cc_final: 0.8727 (mt0) REVERT: E 82 GLU cc_start: 0.9301 (tt0) cc_final: 0.8720 (tm-30) REVERT: F 42 GLN cc_start: 0.8805 (mt0) cc_final: 0.8321 (mp10) REVERT: M 113 ASP cc_start: 0.9103 (p0) cc_final: 0.8851 (p0) REVERT: M 119 GLU cc_start: 0.9566 (mp0) cc_final: 0.9190 (mp0) REVERT: M 362 MET cc_start: 0.8687 (ptp) cc_final: 0.8420 (ptm) REVERT: G 10 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8835 (mm-30) REVERT: G 65 GLN cc_start: 0.8887 (tt0) cc_final: 0.8487 (mt0) REVERT: G 82 GLU cc_start: 0.9305 (tt0) cc_final: 0.8766 (tm-30) REVERT: I 42 GLN cc_start: 0.8792 (mt0) cc_final: 0.8329 (mp10) REVERT: N 113 ASP cc_start: 0.9092 (p0) cc_final: 0.8848 (p0) REVERT: N 119 GLU cc_start: 0.9550 (mp0) cc_final: 0.9164 (mp0) REVERT: N 362 MET cc_start: 0.8683 (ptp) cc_final: 0.8422 (ptm) REVERT: H 10 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8830 (mm-30) REVERT: H 65 GLN cc_start: 0.8961 (tt0) cc_final: 0.8594 (mt0) REVERT: H 82 GLU cc_start: 0.9300 (tt0) cc_final: 0.8737 (tm-30) REVERT: L 42 GLN cc_start: 0.8789 (mt0) cc_final: 0.8325 (mp10) REVERT: O 113 ASP cc_start: 0.9088 (p0) cc_final: 0.8841 (p0) REVERT: O 119 GLU cc_start: 0.9550 (mp0) cc_final: 0.9164 (mp0) REVERT: O 362 MET cc_start: 0.8689 (ptp) cc_final: 0.8425 (ptm) REVERT: J 10 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8843 (mm-30) REVERT: J 65 GLN cc_start: 0.8878 (tt0) cc_final: 0.8474 (mt0) REVERT: J 82 GLU cc_start: 0.9298 (tt0) cc_final: 0.8737 (tm-30) REVERT: K 42 GLN cc_start: 0.8800 (mt0) cc_final: 0.8322 (mp10) REVERT: K 104 LYS cc_start: 0.9444 (tptp) cc_final: 0.9225 (tptt) REVERT: P 119 GLU cc_start: 0.9552 (mp0) cc_final: 0.9168 (mp0) REVERT: P 362 MET cc_start: 0.8684 (ptp) cc_final: 0.8421 (ptm) outliers start: 42 outliers final: 37 residues processed: 361 average time/residue: 0.3784 time to fit residues: 203.9406 Evaluate side-chains 356 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 319 time to evaluate : 2.238 ------------------------------------------------------------------------------- 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 102 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain M residue 109 SER 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 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 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 34 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 90 HIS 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 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN M 347 HIS G 65 GLN I 70 GLN H 65 GLN O 347 HIS J 65 GLN P 347 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20899 Z= 0.415 Angle : 0.697 8.217 28388 Z= 0.353 Chirality : 0.046 0.196 3354 Planarity : 0.004 0.036 3526 Dihedral : 7.631 53.030 4464 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 11.70 % Favored : 85.30 % 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: -0.62 (0.17), residues: 2477 helix: -1.17 (1.00), residues: 28 sheet: -0.40 (0.17), residues: 911 loop : -0.33 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 178 HIS 0.004 0.001 HIS N 347 PHE 0.017 0.002 PHE K 83 TYR 0.015 0.002 TYR H 80 ARG 0.005 0.001 ARG G 19 *********************** 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 394 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 330 time to evaluate : 2.377 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: E 65 GLN cc_start: 0.9213 (tt0) cc_final: 0.8720 (mt0) REVERT: E 82 GLU cc_start: 0.9346 (tt0) cc_final: 0.8677 (tm-30) REVERT: F 42 GLN cc_start: 0.8880 (mt0) cc_final: 0.8334 (mp10) REVERT: F 104 LYS cc_start: 0.9460 (tptt) cc_final: 0.9182 (tptp) REVERT: M 113 ASP cc_start: 0.9125 (p0) cc_final: 0.8838 (p0) REVERT: M 119 GLU cc_start: 0.9560 (mp0) cc_final: 0.9212 (mp0) REVERT: M 362 MET cc_start: 0.8686 (ptp) cc_final: 0.8433 (ptm) REVERT: G 10 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8743 (mm-30) REVERT: G 65 GLN cc_start: 0.8934 (tt0) cc_final: 0.8562 (mt0) REVERT: G 82 GLU cc_start: 0.9349 (tt0) cc_final: 0.8679 (tm-30) REVERT: I 42 GLN cc_start: 0.8862 (mt0) cc_final: 0.8372 (mp10) REVERT: I 101 GLN cc_start: 0.9334 (pm20) cc_final: 0.9116 (pm20) REVERT: N 113 ASP cc_start: 0.9114 (p0) cc_final: 0.8843 (p0) REVERT: N 119 GLU cc_start: 0.9541 (mp0) cc_final: 0.9164 (mp0) REVERT: N 362 MET cc_start: 0.8685 (ptp) cc_final: 0.8436 (ptm) REVERT: H 10 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8737 (mm-30) REVERT: H 65 GLN cc_start: 0.8939 (tt0) cc_final: 0.8575 (mt0) REVERT: H 82 GLU cc_start: 0.9352 (tt0) cc_final: 0.8670 (tm-30) REVERT: L 4 MET cc_start: 0.9238 (tpp) cc_final: 0.8889 (tpp) REVERT: L 42 GLN cc_start: 0.8863 (mt0) cc_final: 0.8373 (mp10) REVERT: L 101 GLN cc_start: 0.9340 (pm20) cc_final: 0.9119 (pm20) REVERT: O 113 ASP cc_start: 0.9110 (p0) cc_final: 0.8838 (p0) REVERT: O 119 GLU cc_start: 0.9544 (mp0) cc_final: 0.9193 (mp0) REVERT: O 362 MET cc_start: 0.8690 (ptp) cc_final: 0.8444 (ptm) REVERT: J 10 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8714 (mm-30) REVERT: J 65 GLN cc_start: 0.8935 (tt0) cc_final: 0.8562 (mt0) REVERT: J 82 GLU cc_start: 0.9349 (tt0) cc_final: 0.8670 (tm-30) REVERT: K 4 MET cc_start: 0.9225 (tpp) cc_final: 0.8902 (tpp) REVERT: K 42 GLN cc_start: 0.8871 (mt0) cc_final: 0.8377 (mp10) REVERT: K 104 LYS cc_start: 0.9410 (tptp) cc_final: 0.9014 (tptp) REVERT: P 119 GLU cc_start: 0.9548 (mp0) cc_final: 0.9199 (mp0) REVERT: P 362 MET cc_start: 0.8686 (ptp) cc_final: 0.8440 (ptm) outliers start: 64 outliers final: 47 residues processed: 362 average time/residue: 0.3538 time to fit residues: 197.0999 Evaluate side-chains 362 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain M residue 109 SER 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 M residue 460 ASP 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 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 52 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 L residue 90 HIS 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 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 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20899 Z= 0.263 Angle : 0.647 8.638 28388 Z= 0.329 Chirality : 0.045 0.207 3354 Planarity : 0.004 0.049 3526 Dihedral : 7.187 57.358 4464 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 2.16 % Allowed : 13.29 % Favored : 84.55 % 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: -1.45 (0.83), residues: 28 sheet: -0.37 (0.17), residues: 918 loop : -0.21 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 178 HIS 0.003 0.001 HIS O 274 PHE 0.012 0.001 PHE O 410 TYR 0.017 0.001 TYR J 80 ARG 0.009 0.001 ARG J 19 *********************** 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 388 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 2.389 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 65 GLN cc_start: 0.9317 (tt0) cc_final: 0.8838 (mt0) REVERT: E 82 GLU cc_start: 0.9364 (tt0) cc_final: 0.8681 (tm-30) REVERT: E 89 GLU cc_start: 0.9510 (pm20) cc_final: 0.9271 (pm20) REVERT: F 4 MET cc_start: 0.9278 (tpp) cc_final: 0.8911 (tpp) REVERT: F 27 ARG cc_start: 0.9255 (ptt90) cc_final: 0.8998 (ptt180) REVERT: F 42 GLN cc_start: 0.8891 (mt0) cc_final: 0.8334 (mp10) REVERT: F 101 GLN cc_start: 0.9356 (pm20) cc_final: 0.9131 (pm20) REVERT: M 113 ASP cc_start: 0.9182 (p0) cc_final: 0.8894 (p0) REVERT: M 119 GLU cc_start: 0.9549 (mp0) cc_final: 0.9228 (mp0) REVERT: M 362 MET cc_start: 0.8613 (ptp) cc_final: 0.8364 (ptm) REVERT: G 10 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8899 (mm-30) REVERT: G 65 GLN cc_start: 0.8983 (tt0) cc_final: 0.8600 (mt0) REVERT: G 82 GLU cc_start: 0.9360 (tt0) cc_final: 0.8693 (tm-30) REVERT: G 89 GLU cc_start: 0.9487 (pm20) cc_final: 0.9259 (pm20) REVERT: I 4 MET cc_start: 0.9279 (tpp) cc_final: 0.8928 (tpp) REVERT: I 42 GLN cc_start: 0.8836 (mt0) cc_final: 0.8366 (mp10) REVERT: I 101 GLN cc_start: 0.9345 (pm20) cc_final: 0.9133 (pm20) REVERT: N 113 ASP cc_start: 0.9181 (p0) cc_final: 0.8897 (p0) REVERT: N 119 GLU cc_start: 0.9538 (mp0) cc_final: 0.9215 (mp0) REVERT: N 362 MET cc_start: 0.8613 (ptp) cc_final: 0.8370 (ptm) REVERT: H 10 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8865 (mm-30) REVERT: H 65 GLN cc_start: 0.8994 (tt0) cc_final: 0.8603 (mt0) REVERT: H 82 GLU cc_start: 0.9359 (tt0) cc_final: 0.8691 (tm-30) REVERT: H 89 GLU cc_start: 0.9490 (pm20) cc_final: 0.9254 (pm20) REVERT: L 42 GLN cc_start: 0.8838 (mt0) cc_final: 0.8367 (mp10) REVERT: L 101 GLN cc_start: 0.9341 (pm20) cc_final: 0.9114 (pm20) REVERT: O 113 ASP cc_start: 0.9174 (p0) cc_final: 0.8884 (p0) REVERT: O 119 GLU cc_start: 0.9537 (mp0) cc_final: 0.9211 (mp0) REVERT: O 362 MET cc_start: 0.8622 (ptp) cc_final: 0.8376 (ptm) REVERT: J 10 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8863 (mm-30) REVERT: J 65 GLN cc_start: 0.8988 (tt0) cc_final: 0.8632 (mt0) REVERT: J 82 GLU cc_start: 0.9363 (tt0) cc_final: 0.8695 (tm-30) REVERT: J 89 GLU cc_start: 0.9488 (pm20) cc_final: 0.9263 (pm20) REVERT: K 42 GLN cc_start: 0.8839 (mt0) cc_final: 0.8368 (mp10) REVERT: P 119 GLU cc_start: 0.9537 (mp0) cc_final: 0.9215 (mp0) REVERT: P 362 MET cc_start: 0.8619 (ptp) cc_final: 0.8372 (ptm) outliers start: 46 outliers final: 36 residues processed: 369 average time/residue: 0.3492 time to fit residues: 195.8264 Evaluate side-chains 352 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 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 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 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 L residue 90 HIS Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20899 Z= 0.270 Angle : 0.656 8.927 28388 Z= 0.332 Chirality : 0.045 0.214 3354 Planarity : 0.004 0.040 3526 Dihedral : 7.010 58.678 4464 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 2.25 % Allowed : 13.34 % Favored : 84.41 % 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: -0.45 (0.17), residues: 2477 helix: -1.10 (0.94), residues: 28 sheet: -0.36 (0.17), residues: 918 loop : -0.14 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 178 HIS 0.003 0.001 HIS O 274 PHE 0.014 0.001 PHE F 83 TYR 0.014 0.001 TYR H 80 ARG 0.011 0.001 ARG J 87 *********************** 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 385 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 2.148 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 65 GLN cc_start: 0.9325 (tt0) cc_final: 0.8831 (mt0) REVERT: E 82 GLU cc_start: 0.9367 (tt0) cc_final: 0.8703 (tm-30) REVERT: E 89 GLU cc_start: 0.9488 (pm20) cc_final: 0.9242 (pm20) REVERT: F 4 MET cc_start: 0.9250 (tpp) cc_final: 0.8977 (tpp) REVERT: F 27 ARG cc_start: 0.9279 (ptt90) cc_final: 0.9022 (ptt180) REVERT: F 42 GLN cc_start: 0.8881 (mt0) cc_final: 0.8348 (mp10) REVERT: F 101 GLN cc_start: 0.9345 (pm20) cc_final: 0.9106 (pm20) REVERT: M 113 ASP cc_start: 0.9186 (p0) cc_final: 0.8919 (p0) REVERT: M 119 GLU cc_start: 0.9534 (mp0) cc_final: 0.9210 (mp0) REVERT: M 362 MET cc_start: 0.8609 (ptp) cc_final: 0.8363 (ptm) REVERT: G 10 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8894 (mm-30) REVERT: G 65 GLN cc_start: 0.8966 (tt0) cc_final: 0.8579 (mt0) REVERT: G 82 GLU cc_start: 0.9348 (tt0) cc_final: 0.8695 (tm-30) REVERT: G 89 GLU cc_start: 0.9496 (pm20) cc_final: 0.9249 (pm20) REVERT: I 4 MET cc_start: 0.9254 (tpp) cc_final: 0.8989 (tpp) REVERT: I 27 ARG cc_start: 0.9270 (ptt90) cc_final: 0.9013 (ptt180) REVERT: I 42 GLN cc_start: 0.8848 (mt0) cc_final: 0.8396 (mp10) REVERT: I 101 GLN cc_start: 0.9340 (pm20) cc_final: 0.9122 (pm20) REVERT: N 113 ASP cc_start: 0.9203 (p0) cc_final: 0.8959 (p0) REVERT: N 119 GLU cc_start: 0.9515 (mp0) cc_final: 0.9191 (mp0) REVERT: N 362 MET cc_start: 0.8604 (ptp) cc_final: 0.8369 (ptm) REVERT: H 10 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8889 (mm-30) REVERT: H 65 GLN cc_start: 0.8997 (tt0) cc_final: 0.8583 (mt0) REVERT: H 82 GLU cc_start: 0.9349 (tt0) cc_final: 0.8689 (tm-30) REVERT: H 89 GLU cc_start: 0.9493 (pm20) cc_final: 0.9247 (pm20) REVERT: L 4 MET cc_start: 0.9276 (tpp) cc_final: 0.8969 (tpp) REVERT: L 42 GLN cc_start: 0.8870 (mt0) cc_final: 0.8419 (mp10) REVERT: L 101 GLN cc_start: 0.9336 (pm20) cc_final: 0.9120 (pm20) REVERT: O 113 ASP cc_start: 0.9184 (p0) cc_final: 0.8900 (p0) REVERT: O 119 GLU cc_start: 0.9516 (mp0) cc_final: 0.9193 (mp0) REVERT: O 362 MET cc_start: 0.8613 (ptp) cc_final: 0.8374 (ptm) REVERT: J 10 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8899 (mm-30) REVERT: J 65 GLN cc_start: 0.8969 (tt0) cc_final: 0.8581 (mt0) REVERT: J 82 GLU cc_start: 0.9352 (tt0) cc_final: 0.8685 (tm-30) REVERT: J 89 GLU cc_start: 0.9493 (pm20) cc_final: 0.9247 (pm20) REVERT: K 4 MET cc_start: 0.9268 (tpp) cc_final: 0.8993 (tpp) REVERT: K 42 GLN cc_start: 0.8863 (mt0) cc_final: 0.8413 (mp10) REVERT: K 104 LYS cc_start: 0.9246 (tptp) cc_final: 0.8915 (tptt) REVERT: P 119 GLU cc_start: 0.9522 (mp0) cc_final: 0.9203 (mp0) REVERT: P 362 MET cc_start: 0.8605 (ptp) cc_final: 0.8367 (ptm) outliers start: 48 outliers final: 39 residues processed: 371 average time/residue: 0.3735 time to fit residues: 208.5146 Evaluate side-chains 364 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain M residue 460 ASP 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 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 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 L residue 90 HIS Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0470 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 184 optimal weight: 8.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20899 Z= 0.229 Angle : 0.650 9.287 28388 Z= 0.329 Chirality : 0.045 0.216 3354 Planarity : 0.004 0.050 3526 Dihedral : 6.875 59.911 4464 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.31 % Favored : 96.53 % Rotamer: Outliers : 2.54 % Allowed : 13.76 % Favored : 83.70 % 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: -1.00 (0.92), residues: 28 sheet: -0.35 (0.17), residues: 938 loop : -0.04 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 178 HIS 0.003 0.001 HIS O 274 PHE 0.032 0.002 PHE L 83 TYR 0.011 0.001 TYR M 121 ARG 0.010 0.001 ARG L 18 *********************** 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 385 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 331 time to evaluate : 2.279 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 65 GLN cc_start: 0.9321 (tt0) cc_final: 0.8956 (mt0) REVERT: E 82 GLU cc_start: 0.9370 (tt0) cc_final: 0.8711 (tm-30) REVERT: E 89 GLU cc_start: 0.9490 (pm20) cc_final: 0.9283 (pm20) REVERT: F 4 MET cc_start: 0.9265 (tpp) cc_final: 0.8997 (tpp) REVERT: F 27 ARG cc_start: 0.9289 (ptt90) cc_final: 0.9034 (ptt180) REVERT: F 42 GLN cc_start: 0.8875 (mt0) cc_final: 0.8373 (mp10) REVERT: F 101 GLN cc_start: 0.9351 (pm20) cc_final: 0.9124 (pm20) REVERT: F 104 LYS cc_start: 0.9330 (tptp) cc_final: 0.8978 (tptp) REVERT: M 113 ASP cc_start: 0.9168 (p0) cc_final: 0.8913 (p0) REVERT: M 119 GLU cc_start: 0.9507 (mp0) cc_final: 0.9175 (mp0) REVERT: M 362 MET cc_start: 0.8569 (ptp) cc_final: 0.8326 (ptm) REVERT: G 10 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8923 (mm-30) REVERT: G 65 GLN cc_start: 0.8984 (tt0) cc_final: 0.8594 (mt0) REVERT: G 82 GLU cc_start: 0.9346 (tt0) cc_final: 0.8724 (tm-30) REVERT: G 89 GLU cc_start: 0.9485 (pm20) cc_final: 0.9268 (pm20) REVERT: I 4 MET cc_start: 0.9273 (tpp) cc_final: 0.9012 (tpp) REVERT: I 27 ARG cc_start: 0.9273 (ptt90) cc_final: 0.9016 (ptt180) REVERT: I 42 GLN cc_start: 0.8823 (mt0) cc_final: 0.8365 (mp10) REVERT: I 101 GLN cc_start: 0.9344 (pm20) cc_final: 0.9121 (pm20) REVERT: N 113 ASP cc_start: 0.9180 (p0) cc_final: 0.8922 (p0) REVERT: N 362 MET cc_start: 0.8564 (ptp) cc_final: 0.8323 (ptm) REVERT: H 10 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8881 (mm-30) REVERT: H 65 GLN cc_start: 0.9007 (tt0) cc_final: 0.8600 (mt0) REVERT: H 82 GLU cc_start: 0.9349 (tt0) cc_final: 0.8707 (tm-30) REVERT: H 89 GLU cc_start: 0.9482 (pm20) cc_final: 0.9266 (pm20) REVERT: L 4 MET cc_start: 0.9304 (tpp) cc_final: 0.9011 (tpp) REVERT: L 42 GLN cc_start: 0.8827 (mt0) cc_final: 0.8378 (mp10) REVERT: L 101 GLN cc_start: 0.9342 (pm20) cc_final: 0.9120 (pm20) REVERT: O 113 ASP cc_start: 0.9179 (p0) cc_final: 0.8913 (p0) REVERT: O 362 MET cc_start: 0.8566 (ptp) cc_final: 0.8325 (ptm) REVERT: J 10 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8905 (mm-30) REVERT: J 65 GLN cc_start: 0.8986 (tt0) cc_final: 0.8595 (mt0) REVERT: J 82 GLU cc_start: 0.9349 (tt0) cc_final: 0.8733 (tm-30) REVERT: J 89 GLU cc_start: 0.9485 (pm20) cc_final: 0.9271 (pm20) REVERT: K 4 MET cc_start: 0.9298 (tpp) cc_final: 0.9024 (tpp) REVERT: K 42 GLN cc_start: 0.8821 (mt0) cc_final: 0.8374 (mp10) REVERT: P 119 GLU cc_start: 0.9505 (mp0) cc_final: 0.9190 (mp0) REVERT: P 362 MET cc_start: 0.8561 (ptp) cc_final: 0.8325 (ptm) outliers start: 54 outliers final: 47 residues processed: 367 average time/residue: 0.3728 time to fit residues: 206.2859 Evaluate side-chains 365 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS 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 M residue 460 ASP 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 230 CYS Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 460 ASP 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 L residue 90 HIS Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 460 ASP 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 P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20899 Z= 0.259 Angle : 0.663 8.933 28388 Z= 0.337 Chirality : 0.045 0.217 3354 Planarity : 0.004 0.043 3526 Dihedral : 6.867 59.821 4464 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 2.72 % Allowed : 13.95 % Favored : 83.33 % 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: -0.39 (0.17), residues: 2477 helix: -0.67 (0.99), residues: 28 sheet: -0.36 (0.17), residues: 946 loop : -0.07 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 178 HIS 0.003 0.001 HIS N 274 PHE 0.031 0.002 PHE F 83 TYR 0.011 0.001 TYR M 121 ARG 0.009 0.001 ARG E 87 *********************** 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 380 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 322 time to evaluate : 2.327 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 65 GLN cc_start: 0.9320 (tt0) cc_final: 0.8950 (mt0) REVERT: E 82 GLU cc_start: 0.9386 (tt0) cc_final: 0.8704 (tm-30) REVERT: F 27 ARG cc_start: 0.9297 (ptt90) cc_final: 0.9039 (ptt180) REVERT: F 42 GLN cc_start: 0.8866 (mt0) cc_final: 0.8367 (mp10) REVERT: F 101 GLN cc_start: 0.9356 (pm20) cc_final: 0.9119 (pm20) REVERT: M 113 ASP cc_start: 0.9173 (p0) cc_final: 0.8958 (p0) REVERT: M 119 GLU cc_start: 0.9500 (mp0) cc_final: 0.9161 (mp0) REVERT: M 198 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9233 (m-30) REVERT: M 362 MET cc_start: 0.8581 (ptp) cc_final: 0.8357 (ptm) REVERT: G 10 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8927 (mm-30) REVERT: G 65 GLN cc_start: 0.9015 (tt0) cc_final: 0.8612 (mt0) REVERT: G 82 GLU cc_start: 0.9365 (tt0) cc_final: 0.8734 (tm-30) REVERT: G 89 GLU cc_start: 0.9481 (pm20) cc_final: 0.9278 (pm20) REVERT: I 4 MET cc_start: 0.9249 (tpp) cc_final: 0.9014 (tpp) REVERT: I 27 ARG cc_start: 0.9289 (ptt90) cc_final: 0.9035 (ptt180) REVERT: I 42 GLN cc_start: 0.8822 (mt0) cc_final: 0.8354 (mp10) REVERT: I 101 GLN cc_start: 0.9347 (pm20) cc_final: 0.9129 (pm20) REVERT: N 113 ASP cc_start: 0.9175 (p0) cc_final: 0.8962 (p0) REVERT: N 119 GLU cc_start: 0.9470 (mp0) cc_final: 0.9242 (mp0) REVERT: N 362 MET cc_start: 0.8572 (ptp) cc_final: 0.8348 (ptm) REVERT: H 10 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8924 (mm-30) REVERT: H 23 LYS cc_start: 0.9667 (tptp) cc_final: 0.9455 (tptp) REVERT: H 65 GLN cc_start: 0.9011 (tt0) cc_final: 0.8597 (mt0) REVERT: H 82 GLU cc_start: 0.9369 (tt0) cc_final: 0.8730 (tm-30) REVERT: H 89 GLU cc_start: 0.9476 (pm20) cc_final: 0.9270 (pm20) REVERT: L 4 MET cc_start: 0.9287 (tpp) cc_final: 0.9021 (tpp) REVERT: L 42 GLN cc_start: 0.8823 (mt0) cc_final: 0.8356 (mp10) REVERT: L 101 GLN cc_start: 0.9343 (pm20) cc_final: 0.9126 (pm20) REVERT: O 113 ASP cc_start: 0.9172 (p0) cc_final: 0.8939 (p0) REVERT: O 119 GLU cc_start: 0.9470 (mp0) cc_final: 0.9239 (mp0) REVERT: O 362 MET cc_start: 0.8580 (ptp) cc_final: 0.8358 (ptm) REVERT: J 10 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8897 (mm-30) REVERT: J 65 GLN cc_start: 0.9010 (tt0) cc_final: 0.8604 (mt0) REVERT: J 82 GLU cc_start: 0.9367 (tt0) cc_final: 0.8732 (tm-30) REVERT: J 89 GLU cc_start: 0.9478 (pm20) cc_final: 0.9276 (pm20) REVERT: K 4 MET cc_start: 0.9278 (tpp) cc_final: 0.8985 (tpp) REVERT: K 42 GLN cc_start: 0.8828 (mt0) cc_final: 0.8354 (mp10) REVERT: K 104 LYS cc_start: 0.9233 (tptp) cc_final: 0.8894 (tptp) REVERT: P 119 GLU cc_start: 0.9502 (mp0) cc_final: 0.9186 (mp0) REVERT: P 362 MET cc_start: 0.8576 (ptp) cc_final: 0.8353 (ptm) outliers start: 58 outliers final: 49 residues processed: 361 average time/residue: 0.3575 time to fit residues: 197.1583 Evaluate side-chains 366 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 90 HIS 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 M residue 460 ASP 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 140 LEU Chi-restraints excluded: chain N residue 157 THR 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 460 ASP 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 L residue 90 HIS 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 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 460 ASP 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 P residue 157 THR Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20899 Z= 0.347 Angle : 0.699 8.076 28388 Z= 0.354 Chirality : 0.046 0.216 3354 Planarity : 0.004 0.064 3526 Dihedral : 7.000 59.013 4464 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 2.49 % Allowed : 14.94 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.37 (0.17), residues: 2477 helix: -0.37 (1.06), residues: 28 sheet: -0.30 (0.17), residues: 923 loop : -0.11 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 178 HIS 0.003 0.001 HIS N 274 PHE 0.038 0.002 PHE K 83 TYR 0.021 0.001 TYR E 80 ARG 0.012 0.001 ARG E 87 ********************** 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 362 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 GLN cc_start: 0.9331 (tt0) cc_final: 0.8957 (mt0) REVERT: E 82 GLU cc_start: 0.9373 (tt0) cc_final: 0.8712 (tm-30) REVERT: F 4 MET cc_start: 0.9259 (tpp) cc_final: 0.8914 (tpp) REVERT: F 27 ARG cc_start: 0.9303 (ptt90) cc_final: 0.9047 (ptt180) REVERT: F 42 GLN cc_start: 0.8896 (mt0) cc_final: 0.8389 (mp10) REVERT: F 101 GLN cc_start: 0.9353 (pm20) cc_final: 0.9102 (pm20) REVERT: M 113 ASP cc_start: 0.9183 (p0) cc_final: 0.8961 (p0) REVERT: M 119 GLU cc_start: 0.9518 (mp0) cc_final: 0.9184 (mp0) REVERT: M 198 ASP cc_start: 0.9459 (OUTLIER) cc_final: 0.9210 (m-30) REVERT: M 362 MET cc_start: 0.8637 (ptp) cc_final: 0.8409 (ptm) REVERT: G 10 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8935 (mm-30) REVERT: G 23 LYS cc_start: 0.9668 (tptp) cc_final: 0.9457 (tptp) REVERT: G 65 GLN cc_start: 0.9012 (tt0) cc_final: 0.8622 (mt0) REVERT: G 82 GLU cc_start: 0.9351 (tt0) cc_final: 0.8697 (tm-30) REVERT: I 27 ARG cc_start: 0.9281 (ptt90) cc_final: 0.9023 (ptt180) REVERT: I 42 GLN cc_start: 0.8870 (mt0) cc_final: 0.8389 (mp10) REVERT: I 101 GLN cc_start: 0.9346 (pm20) cc_final: 0.9123 (pm20) REVERT: N 113 ASP cc_start: 0.9190 (p0) cc_final: 0.8963 (p0) REVERT: N 119 GLU cc_start: 0.9465 (mp0) cc_final: 0.9220 (mp0) REVERT: N 362 MET cc_start: 0.8634 (ptp) cc_final: 0.8408 (ptm) REVERT: H 10 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8924 (mm-30) REVERT: H 19 ARG cc_start: 0.9531 (mmm-85) cc_final: 0.9304 (mmm160) REVERT: H 65 GLN cc_start: 0.9019 (tt0) cc_final: 0.8615 (mt0) REVERT: H 82 GLU cc_start: 0.9364 (tt0) cc_final: 0.8699 (tm-30) REVERT: H 89 GLU cc_start: 0.9476 (pm20) cc_final: 0.9264 (pm20) REVERT: L 4 MET cc_start: 0.9252 (tpp) cc_final: 0.8961 (tpp) REVERT: L 42 GLN cc_start: 0.8868 (mt0) cc_final: 0.8399 (mp10) REVERT: L 101 GLN cc_start: 0.9337 (pm20) cc_final: 0.9116 (pm20) REVERT: L 106 GLU cc_start: 0.9101 (pt0) cc_final: 0.8760 (pm20) REVERT: L 108 LYS cc_start: 0.8985 (tppt) cc_final: 0.8683 (tmtt) REVERT: O 113 ASP cc_start: 0.9185 (p0) cc_final: 0.8943 (p0) REVERT: O 119 GLU cc_start: 0.9464 (mp0) cc_final: 0.9221 (mp0) REVERT: O 362 MET cc_start: 0.8636 (ptp) cc_final: 0.8412 (ptm) REVERT: J 10 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8905 (mm-30) REVERT: J 23 LYS cc_start: 0.9666 (tptp) cc_final: 0.9459 (tptp) REVERT: J 65 GLN cc_start: 0.9025 (tt0) cc_final: 0.8663 (mt0) REVERT: J 82 GLU cc_start: 0.9353 (tt0) cc_final: 0.8700 (tm-30) REVERT: K 4 MET cc_start: 0.9241 (tpp) cc_final: 0.8971 (tpp) REVERT: K 42 GLN cc_start: 0.8875 (mt0) cc_final: 0.8402 (mp10) REVERT: P 119 GLU cc_start: 0.9517 (mp0) cc_final: 0.9208 (mp0) REVERT: P 362 MET cc_start: 0.8633 (ptp) cc_final: 0.8406 (ptm) outliers start: 53 outliers final: 49 residues processed: 345 average time/residue: 0.3479 time to fit residues: 182.8963 Evaluate side-chains 357 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 HIS 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 M residue 460 ASP 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 140 LEU Chi-restraints excluded: chain N residue 157 THR 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 460 ASP 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 L residue 90 HIS 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 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 460 ASP 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 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 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 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049855 restraints weight = 60559.576| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.79 r_work: 0.2690 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20899 Z= 0.245 Angle : 0.676 8.242 28388 Z= 0.342 Chirality : 0.045 0.217 3354 Planarity : 0.004 0.072 3526 Dihedral : 6.845 59.665 4464 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 2.35 % Allowed : 15.03 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.17), residues: 2477 helix: -0.47 (1.02), residues: 28 sheet: -0.29 (0.17), residues: 938 loop : -0.02 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 178 HIS 0.003 0.001 HIS O 274 PHE 0.034 0.002 PHE F 83 TYR 0.011 0.001 TYR G 80 ARG 0.011 0.001 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.26 seconds wall clock time: 88 minutes 18.71 seconds (5298.71 seconds total)