Starting phenix.real_space_refine on Sat Jul 4 12:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.map" model { file = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g30_29686/07_2026/8g30_29686.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12715 2.51 5 N 3422 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20449 Number of models: 1 Model: "" Number of chains: 40 Chain: "E" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2972 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 367} Chain breaks: 1 Chain: "G" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "P" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 4.33, per 1000 atoms: 0.21 Number of scatterers: 20449 At special positions: 0 Unit cell: (165.933, 165.933, 105.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4191 8.00 N 3422 7.00 C 12715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.06 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 92 " - pdb=" SG CYS M 417 " distance=2.06 Simple disulfide: pdb=" SG CYS M 124 " - pdb=" SG CYS M 129 " distance=2.07 Simple disulfide: pdb=" SG CYS M 175 " - pdb=" SG CYS M 193 " distance=2.01 Simple disulfide: pdb=" SG CYS M 183 " - pdb=" SG CYS M 230 " distance=2.08 Simple disulfide: pdb=" SG CYS M 232 " - pdb=" SG CYS M 237 " distance=2.07 Simple disulfide: pdb=" SG CYS M 278 " - pdb=" SG CYS M 291 " distance=2.01 Simple disulfide: pdb=" SG CYS M 280 " - pdb=" SG CYS M 289 " distance=2.08 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.07 Simple disulfide: pdb=" SG CYS M 421 " - pdb=" SG CYS M 447 " distance=2.09 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.06 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 417 " distance=2.05 Simple disulfide: pdb=" SG CYS N 124 " - pdb=" SG CYS N 129 " distance=2.07 Simple disulfide: pdb=" SG CYS N 175 " - pdb=" SG CYS N 193 " distance=2.01 Simple disulfide: pdb=" SG CYS N 183 " - pdb=" SG CYS N 230 " distance=2.08 Simple disulfide: pdb=" SG CYS N 232 " - pdb=" SG CYS N 237 " distance=2.07 Simple disulfide: pdb=" SG CYS N 278 " - pdb=" SG CYS N 291 " distance=2.01 Simple disulfide: pdb=" SG CYS N 280 " - pdb=" SG CYS N 289 " distance=2.08 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.06 Simple disulfide: pdb=" SG CYS N 421 " - pdb=" SG CYS N 447 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 417 " distance=2.05 Simple disulfide: pdb=" SG CYS O 124 " - pdb=" SG CYS O 129 " distance=2.07 Simple disulfide: pdb=" SG CYS O 175 " - pdb=" SG CYS O 193 " distance=2.01 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 230 " distance=2.07 Simple disulfide: pdb=" SG CYS O 232 " - pdb=" SG CYS O 237 " distance=2.07 Simple disulfide: pdb=" SG CYS O 278 " - pdb=" SG CYS O 291 " distance=2.01 Simple disulfide: pdb=" SG CYS O 280 " - pdb=" SG CYS O 289 " distance=2.08 Simple disulfide: pdb=" SG CYS O 318 " - pdb=" SG CYS O 337 " distance=2.06 Simple disulfide: pdb=" SG CYS O 421 " - pdb=" SG CYS O 447 " distance=2.09 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS P 92 " - pdb=" SG CYS P 417 " distance=2.05 Simple disulfide: pdb=" SG CYS P 124 " - pdb=" SG CYS P 129 " distance=2.07 Simple disulfide: pdb=" SG CYS P 175 " - pdb=" SG CYS P 193 " distance=2.01 Simple disulfide: pdb=" SG CYS P 183 " - pdb=" SG CYS P 230 " distance=2.07 Simple disulfide: pdb=" SG CYS P 232 " - pdb=" SG CYS P 237 " distance=2.07 Simple disulfide: pdb=" SG CYS P 278 " - pdb=" SG CYS P 291 " distance=2.01 Simple disulfide: pdb=" SG CYS P 280 " - pdb=" SG CYS P 289 " distance=2.08 Simple disulfide: pdb=" SG CYS P 318 " - pdb=" SG CYS P 337 " distance=2.06 Simple disulfide: pdb=" SG CYS P 421 " - pdb=" SG CYS P 447 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG 1 1 " - " ASN P 86 " " NAG 2 1 " - " ASN P 146 " " NAG 3 1 " - " ASN P 200 " " NAG 4 1 " - " ASN P 234 " " NAG 6 1 " - " ASN P 329 " " NAG 7 1 " - " ASN P 367 " " NAG a 1 " - " ASN M 86 " " NAG b 1 " - " ASN M 146 " " NAG c 1 " - " ASN M 200 " " NAG d 1 " - " ASN M 234 " " NAG f 1 " - " ASN M 329 " " NAG g 1 " - " ASN M 367 " " NAG i 1 " - " ASN N 86 " " NAG j 1 " - " ASN N 146 " " NAG k 1 " - " ASN N 200 " " NAG l 1 " - " ASN N 234 " " NAG n 1 " - " ASN N 329 " " NAG o 1 " - " ASN N 367 " " NAG q 1 " - " ASN O 86 " " NAG r 1 " - " ASN O 146 " " NAG s 1 " - " ASN O 200 " " NAG t 1 " - " ASN O 234 " " NAG v 1 " - " ASN O 329 " " NAG w 1 " - " ASN O 367 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 863.1 milliseconds 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 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: 3.76 Time building geometry restraints manager: 2.68 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 - 17.63: 10864 17.63 - 35.26: 688 35.26 - 52.89: 124 52.89 - 70.52: 40 70.52 - 88.15: 20 Dihedral angle restraints: 11736 sinusoidal: 4606 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 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1650 0.065 - 0.130: 1109 0.130 - 0.195: 461 0.195 - 0.259: 119 0.259 - 0.324: 15 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.67e+01 ... (remaining 3351 not shown) Planarity restraints: 3550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 121 " -0.116 2.00e-02 2.50e+03 6.06e-02 7.34e+01 pdb=" CG TYR N 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR N 121 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR N 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR N 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR N 121 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR N 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 121 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 121 " 0.116 2.00e-02 2.50e+03 6.05e-02 7.32e+01 pdb=" CG TYR O 121 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR O 121 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR O 121 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR O 121 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR O 121 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR O 121 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 121 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 121 " -0.116 2.00e-02 2.50e+03 6.04e-02 7.30e+01 pdb=" CG TYR P 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR P 121 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR P 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR P 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR P 121 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR P 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 121 " -0.081 2.00e-02 2.50e+03 ... (remaining 3547 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1956 2.75 - 3.29: 20789 3.29 - 3.83: 34655 3.83 - 4.36: 47087 4.36 - 4.90: 76572 Nonbonded interactions: 181059 Sorted by model distance: nonbonded pdb=" O GLY N 345 " pdb="CA CA N2000 " model vdw 2.213 2.510 nonbonded pdb=" O GLY P 345 " pdb="CA CA P2000 " model vdw 2.214 2.510 nonbonded pdb=" O GLY O 345 " pdb="CA CA O2000 " model vdw 2.214 2.510 nonbonded pdb=" O HIS M 347 " pdb="CA CA M 501 " model vdw 2.236 2.510 nonbonded pdb=" O HIS O 347 " pdb="CA CA O2000 " model vdw 2.237 2.510 ... (remaining 181054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain 'a' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '6' selection = chain '7' selection = chain 'f' selection = chain 'g' selection = chain 'n' selection = chain 'o' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 82 through 501) selection = (chain 'N' and (resid 82 through 244 or resid 250 through 2000)) selection = (chain 'O' and (resid 82 through 244 or resid 250 through 2000)) selection = (chain 'P' and (resid 82 through 244 or resid 250 through 2000)) } ncs_group { reference = chain 'b' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 19.410 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.075 21029 Z= 1.083 Angle : 1.910 48.443 28734 Z= 1.226 Chirality : 0.095 0.324 3354 Planarity : 0.012 0.073 3526 Dihedral : 13.157 88.150 7060 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.22 % Favored : 93.46 % Rotamer: Outliers : 0.56 % Allowed : 2.91 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 2477 helix: -3.10 (0.72), residues: 28 sheet: -0.77 (0.16), residues: 918 loop : -1.56 (0.14), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG M 224 TYR 0.116 0.016 TYR N 121 PHE 0.087 0.013 PHE O 205 TRP 0.081 0.016 TRP M 458 HIS 0.024 0.005 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01577 / 1.08 (20899) covalent geometry : angle 1.86663 / 1.22 (28388) SS BOND : bond 0.03542 / 2.40 ( 44) SS BOND : angle 2.31605 / 1.54 ( 88) hydrogen bonds : bond 0.14365 / 9.77 ( 643) hydrogen bonds : angle 8.61819 / 5.99 ( 1632) link_ALPHA1-2 : bond 0.00193 / 0.10 ( 4) link_ALPHA1-2 : angle 4.58169 / 2.65 ( 12) link_ALPHA1-3 : bond 0.02071 / 1.04 ( 8) link_ALPHA1-3 : angle 3.04705 / 1.85 ( 24) link_ALPHA1-6 : bond 0.01246 / 0.67 ( 10) link_ALPHA1-6 : angle 3.01511 / 1.67 ( 30) link_BETA1-4 : bond 0.01271 / 0.83 ( 40) link_BETA1-4 : angle 4.34875 / 2.91 ( 120) link_NAG-ASN : bond 0.02409 / 1.28 ( 24) link_NAG-ASN : angle 5.86405 / 3.69 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 448 time to evaluate : 0.760 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: 0.1620 time to fit residues: 108.4529 Evaluate side-chains 353 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain M residue 178 TRP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain N residue 178 TRP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain O residue 178 TRP Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain P residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN M 147 ASN M 391 GLN G 62 GLN N 147 ASN H 62 GLN O 147 ASN O 391 GLN J 62 GLN P 147 ASN P 391 GLN ** P 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051910 restraints weight = 60323.689| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.80 r_work: 0.2655 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21029 Z= 0.178 Angle : 0.769 7.238 28734 Z= 0.393 Chirality : 0.047 0.174 3354 Planarity : 0.004 0.036 3526 Dihedral : 6.692 41.349 2742 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 0.94 % Allowed : 9.82 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2477 helix: -2.18 (0.79), residues: 28 sheet: -0.10 (0.18), residues: 886 loop : -0.72 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.018 0.002 TYR O 121 PHE 0.022 0.002 PHE I 83 TRP 0.020 0.002 TRP O 115 HIS 0.002 0.001 HIS M 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (20899) covalent geometry : angle 0.74212 / 0.39 (28388) SS BOND : bond 0.00353 / 0.21 ( 44) SS BOND : angle 0.73468 / 0.41 ( 88) hydrogen bonds : bond 0.04513 / 2.95 ( 643) hydrogen bonds : angle 7.39278 / 5.20 ( 1632) link_ALPHA1-2 : bond 0.00751 / 0.36 ( 4) link_ALPHA1-2 : angle 1.79460 / 0.91 ( 12) link_ALPHA1-3 : bond 0.00811 / 0.40 ( 8) link_ALPHA1-3 : angle 1.60568 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00689 / 0.38 ( 10) link_ALPHA1-6 : angle 1.28642 / 0.77 ( 30) link_BETA1-4 : bond 0.00442 / 0.28 ( 40) link_BETA1-4 : angle 2.21349 / 1.50 ( 120) link_NAG-ASN : bond 0.00292 / 0.18 ( 24) link_NAG-ASN : angle 2.82707 / 1.82 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 385 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8175 (mm-40) REVERT: E 23 LYS cc_start: 0.9191 (tptm) cc_final: 0.8987 (tptp) REVERT: E 31 LYS cc_start: 0.8664 (tttp) cc_final: 0.8314 (tttm) REVERT: E 65 GLN cc_start: 0.8186 (tt0) cc_final: 0.7728 (mt0) REVERT: E 81 MET cc_start: 0.9380 (ttp) cc_final: 0.8509 (tmm) REVERT: E 82 GLU cc_start: 0.8514 (tt0) cc_final: 0.7928 (tm-30) REVERT: E 89 GLU cc_start: 0.9554 (mp0) cc_final: 0.9263 (pm20) REVERT: F 11 LEU cc_start: 0.9092 (tp) cc_final: 0.8519 (tp) REVERT: F 42 GLN cc_start: 0.7974 (mt0) cc_final: 0.7725 (mp10) REVERT: F 48 ILE cc_start: 0.8913 (mm) cc_final: 0.8699 (mm) REVERT: F 54 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7704 (mtm-85) REVERT: F 70 GLN cc_start: 0.8687 (mm110) cc_final: 0.8380 (mm-40) REVERT: F 83 PHE cc_start: 0.7410 (m-80) cc_final: 0.7152 (m-80) REVERT: F 104 LYS cc_start: 0.8517 (tppt) cc_final: 0.8145 (tptt) REVERT: M 113 ASP cc_start: 0.8756 (p0) cc_final: 0.8408 (p0) REVERT: M 119 GLU cc_start: 0.9028 (mp0) cc_final: 0.8484 (mp0) REVERT: G 3 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8174 (mm-40) REVERT: G 23 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9011 (tptp) REVERT: G 65 GLN cc_start: 0.7848 (tt0) cc_final: 0.7553 (mt0) REVERT: G 81 MET cc_start: 0.9365 (ttp) cc_final: 0.8509 (tmm) REVERT: G 82 GLU cc_start: 0.8533 (tt0) cc_final: 0.7976 (tm-30) REVERT: I 42 GLN cc_start: 0.8026 (mt0) cc_final: 0.7764 (mp10) REVERT: I 54 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7702 (mtm-85) REVERT: I 70 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: I 79 GLN cc_start: 0.9188 (mm110) cc_final: 0.8772 (mm110) REVERT: I 89 GLN cc_start: 0.9324 (tm-30) cc_final: 0.9119 (tt0) REVERT: N 113 ASP cc_start: 0.8718 (p0) cc_final: 0.8361 (p0) REVERT: N 119 GLU cc_start: 0.9092 (mp0) cc_final: 0.8532 (mp0) REVERT: N 402 ASN cc_start: 0.8317 (m-40) cc_final: 0.8114 (m-40) REVERT: H 3 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8173 (mm-40) REVERT: H 23 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9001 (tptp) REVERT: H 65 GLN cc_start: 0.7835 (tt0) cc_final: 0.7536 (mt0) REVERT: H 81 MET cc_start: 0.9353 (ttp) cc_final: 0.8481 (tmm) REVERT: H 82 GLU cc_start: 0.8520 (tt0) cc_final: 0.7961 (tm-30) REVERT: L 42 GLN cc_start: 0.8048 (mt0) cc_final: 0.7777 (mp10) REVERT: L 54 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7684 (mtm-85) REVERT: L 70 GLN cc_start: 0.8707 (mm110) cc_final: 0.8396 (mm110) REVERT: L 78 LEU cc_start: 0.8592 (mp) cc_final: 0.8385 (mp) REVERT: L 79 GLN cc_start: 0.9180 (mm110) cc_final: 0.8759 (mm110) REVERT: O 113 ASP cc_start: 0.8722 (p0) cc_final: 0.8362 (p0) REVERT: O 119 GLU cc_start: 0.9077 (mp0) cc_final: 0.8517 (mp0) REVERT: O 402 ASN cc_start: 0.8302 (m-40) cc_final: 0.8097 (m-40) REVERT: J 3 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8193 (mm-40) REVERT: J 13 ARG cc_start: 0.9214 (mmm160) cc_final: 0.8561 (mmt180) REVERT: J 23 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.9016 (tptp) REVERT: J 65 GLN cc_start: 0.7844 (tt0) cc_final: 0.7546 (mt0) REVERT: J 81 MET cc_start: 0.9363 (ttp) cc_final: 0.8507 (tmm) REVERT: J 82 GLU cc_start: 0.8527 (tt0) cc_final: 0.7969 (tm-30) REVERT: K 42 GLN cc_start: 0.8021 (mt0) cc_final: 0.7761 (mp10) REVERT: K 54 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: K 70 GLN cc_start: 0.8654 (mm110) cc_final: 0.8346 (mm110) REVERT: K 89 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9107 (tt0) REVERT: K 106 GLU cc_start: 0.8013 (tp30) cc_final: 0.7795 (tm-30) REVERT: K 107 ILE cc_start: 0.9397 (mp) cc_final: 0.9190 (pt) REVERT: P 113 ASP cc_start: 0.8724 (p0) cc_final: 0.8374 (p0) REVERT: P 119 GLU cc_start: 0.9075 (mp0) cc_final: 0.8524 (mp0) REVERT: P 402 ASN cc_start: 0.8302 (m-40) cc_final: 0.8098 (m-40) outliers start: 20 outliers final: 11 residues processed: 392 average time/residue: 0.1587 time to fit residues: 91.6557 Evaluate side-chains 356 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 341 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain P residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051896 restraints weight = 60846.319| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.90 r_work: 0.2670 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21029 Z= 0.154 Angle : 0.680 8.549 28734 Z= 0.343 Chirality : 0.044 0.154 3354 Planarity : 0.004 0.045 3526 Dihedral : 5.723 24.404 2726 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.74 % Allowed : 11.18 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2477 helix: -1.81 (0.84), residues: 28 sheet: -0.20 (0.17), residues: 922 loop : -0.36 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.019 0.002 TYR M 121 PHE 0.015 0.002 PHE P 410 TRP 0.018 0.002 TRP N 115 HIS 0.003 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (20899) covalent geometry : angle 0.66016 / 0.34 (28388) SS BOND : bond 0.00287 / 0.17 ( 44) SS BOND : angle 0.49400 / 0.30 ( 88) hydrogen bonds : bond 0.03842 / 2.51 ( 643) hydrogen bonds : angle 6.75195 / 4.74 ( 1632) link_ALPHA1-2 : bond 0.00740 / 0.35 ( 4) link_ALPHA1-2 : angle 1.90260 / 0.96 ( 12) link_ALPHA1-3 : bond 0.00496 / 0.24 ( 8) link_ALPHA1-3 : angle 1.57948 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00486 / 0.26 ( 10) link_ALPHA1-6 : angle 1.41345 / 0.84 ( 30) link_BETA1-4 : bond 0.00466 / 0.28 ( 40) link_BETA1-4 : angle 1.76180 / 1.21 ( 120) link_NAG-ASN : bond 0.00157 / 0.09 ( 24) link_NAG-ASN : angle 2.20289 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8270 (mm-30) REVERT: E 23 LYS cc_start: 0.9204 (tptm) cc_final: 0.8958 (tptm) REVERT: E 65 GLN cc_start: 0.8432 (tt0) cc_final: 0.7935 (mt0) REVERT: E 81 MET cc_start: 0.9343 (ttp) cc_final: 0.8656 (tmm) REVERT: E 82 GLU cc_start: 0.8577 (tt0) cc_final: 0.7942 (tm-30) REVERT: F 4 MET cc_start: 0.9052 (tpp) cc_final: 0.8608 (tpp) REVERT: F 42 GLN cc_start: 0.8119 (mt0) cc_final: 0.7813 (mp10) REVERT: F 54 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7850 (mtm-85) REVERT: F 70 GLN cc_start: 0.8642 (mm110) cc_final: 0.8280 (mm110) REVERT: F 101 GLN cc_start: 0.7833 (pm20) cc_final: 0.7607 (pm20) REVERT: M 113 ASP cc_start: 0.8774 (p0) cc_final: 0.8314 (p0) REVERT: M 119 GLU cc_start: 0.9042 (mp0) cc_final: 0.8447 (mp0) REVERT: M 241 MET cc_start: 0.9404 (mtp) cc_final: 0.9063 (mtm) REVERT: M 362 MET cc_start: 0.8130 (ptp) cc_final: 0.7723 (ptm) REVERT: G 10 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8089 (mm-30) REVERT: G 23 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8898 (tptp) REVERT: G 65 GLN cc_start: 0.8091 (tt0) cc_final: 0.7764 (mt0) REVERT: G 81 MET cc_start: 0.9332 (ttp) cc_final: 0.8997 (tmm) REVERT: G 82 GLU cc_start: 0.8565 (tt0) cc_final: 0.7916 (tm-30) REVERT: G 89 GLU cc_start: 0.9091 (pm20) cc_final: 0.8829 (pm20) REVERT: I 4 MET cc_start: 0.9031 (tpp) cc_final: 0.8582 (tpp) REVERT: I 42 GLN cc_start: 0.8105 (mt0) cc_final: 0.7836 (mp10) REVERT: I 54 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7832 (mtm-85) REVERT: I 70 GLN cc_start: 0.8761 (mt0) cc_final: 0.8304 (mm-40) REVERT: I 89 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8920 (tt0) REVERT: I 101 GLN cc_start: 0.7826 (pm20) cc_final: 0.7592 (pm20) REVERT: I 104 LYS cc_start: 0.8832 (tptp) cc_final: 0.8588 (tptt) REVERT: N 113 ASP cc_start: 0.8745 (p0) cc_final: 0.8271 (p0) REVERT: N 119 GLU cc_start: 0.9052 (mp0) cc_final: 0.8243 (mp0) REVERT: N 241 MET cc_start: 0.9398 (mtp) cc_final: 0.9017 (mtm) REVERT: N 362 MET cc_start: 0.8122 (ptp) cc_final: 0.7726 (ptm) REVERT: H 10 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8098 (mm-30) REVERT: H 23 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8896 (tptp) REVERT: H 46 GLU cc_start: 0.8483 (tt0) cc_final: 0.8167 (tt0) REVERT: H 65 GLN cc_start: 0.8049 (tt0) cc_final: 0.7747 (mt0) REVERT: H 81 MET cc_start: 0.9312 (ttp) cc_final: 0.8972 (tmm) REVERT: H 82 GLU cc_start: 0.8561 (tt0) cc_final: 0.7891 (tm-30) REVERT: H 89 GLU cc_start: 0.9096 (pm20) cc_final: 0.8835 (pm20) REVERT: L 4 MET cc_start: 0.9059 (tpp) cc_final: 0.8619 (tpp) REVERT: L 42 GLN cc_start: 0.8133 (mt0) cc_final: 0.7857 (mp10) REVERT: L 54 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: L 70 GLN cc_start: 0.8698 (mm110) cc_final: 0.8369 (mm110) REVERT: L 101 GLN cc_start: 0.7847 (pm20) cc_final: 0.7605 (pm20) REVERT: L 104 LYS cc_start: 0.8838 (tptp) cc_final: 0.8606 (tptt) REVERT: O 113 ASP cc_start: 0.8740 (p0) cc_final: 0.8251 (p0) REVERT: O 119 GLU cc_start: 0.9045 (mp0) cc_final: 0.8235 (mp0) REVERT: O 241 MET cc_start: 0.9394 (mtp) cc_final: 0.9006 (mtm) REVERT: O 362 MET cc_start: 0.8133 (ptp) cc_final: 0.7721 (ptm) REVERT: J 10 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8090 (mm-30) REVERT: J 23 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: J 65 GLN cc_start: 0.8077 (tt0) cc_final: 0.7755 (mt0) REVERT: J 81 MET cc_start: 0.9322 (ttp) cc_final: 0.8984 (tmm) REVERT: J 82 GLU cc_start: 0.8566 (tt0) cc_final: 0.7918 (tm-30) REVERT: J 89 GLU cc_start: 0.9092 (pm20) cc_final: 0.8833 (pm20) REVERT: K 4 MET cc_start: 0.9077 (tpp) cc_final: 0.8615 (tpp) REVERT: K 42 GLN cc_start: 0.8121 (mt0) cc_final: 0.7849 (mp10) REVERT: K 54 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: K 70 GLN cc_start: 0.8677 (mm110) cc_final: 0.8350 (mm110) REVERT: K 101 GLN cc_start: 0.7821 (pm20) cc_final: 0.7586 (pm20) REVERT: P 113 ASP cc_start: 0.8756 (p0) cc_final: 0.7907 (p0) REVERT: P 119 GLU cc_start: 0.9069 (mp0) cc_final: 0.8353 (mp0) REVERT: P 241 MET cc_start: 0.9398 (mtp) cc_final: 0.9013 (mtm) REVERT: P 362 MET cc_start: 0.8116 (ptp) cc_final: 0.7712 (ptm) outliers start: 37 outliers final: 31 residues processed: 373 average time/residue: 0.1469 time to fit residues: 82.4004 Evaluate side-chains 373 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 LYS 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 H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 63 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 219 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.052004 restraints weight = 60833.115| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.87 r_work: 0.2672 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21029 Z= 0.150 Angle : 0.644 9.230 28734 Z= 0.323 Chirality : 0.043 0.148 3354 Planarity : 0.004 0.036 3526 Dihedral : 5.376 21.197 2726 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 1.64 % Allowed : 12.59 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2477 helix: -1.74 (0.85), residues: 28 sheet: -0.21 (0.17), residues: 926 loop : -0.17 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 87 TYR 0.013 0.001 TYR E 80 PHE 0.012 0.001 PHE M 410 TRP 0.015 0.001 TRP N 178 HIS 0.003 0.001 HIS N 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (20899) covalent geometry : angle 0.62623 / 0.32 (28388) SS BOND : bond 0.00258 / 0.15 ( 44) SS BOND : angle 0.41342 / 0.26 ( 88) hydrogen bonds : bond 0.03534 / 2.31 ( 643) hydrogen bonds : angle 6.49026 / 4.56 ( 1632) link_ALPHA1-2 : bond 0.00732 / 0.35 ( 4) link_ALPHA1-2 : angle 1.83465 / 0.92 ( 12) link_ALPHA1-3 : bond 0.00463 / 0.23 ( 8) link_ALPHA1-3 : angle 1.52538 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00433 / 0.23 ( 10) link_ALPHA1-6 : angle 1.41917 / 0.84 ( 30) link_BETA1-4 : bond 0.00371 / 0.23 ( 40) link_BETA1-4 : angle 1.63782 / 1.13 ( 120) link_NAG-ASN : bond 0.00160 / 0.09 ( 24) link_NAG-ASN : angle 1.99653 / 1.28 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 362 time to evaluate : 0.730 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 10 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8352 (mm-30) REVERT: E 23 LYS cc_start: 0.9184 (tptm) cc_final: 0.8940 (tptm) REVERT: E 46 GLU cc_start: 0.8483 (tt0) cc_final: 0.8211 (tt0) REVERT: E 63 LYS cc_start: 0.9578 (mtpp) cc_final: 0.9276 (mttp) REVERT: E 65 GLN cc_start: 0.8397 (tt0) cc_final: 0.7892 (mt0) REVERT: E 80 TYR cc_start: 0.8764 (m-10) cc_final: 0.8513 (m-10) REVERT: E 81 MET cc_start: 0.9338 (ttp) cc_final: 0.8996 (tmm) REVERT: E 82 GLU cc_start: 0.8616 (tt0) cc_final: 0.7966 (tm-30) REVERT: E 89 GLU cc_start: 0.9177 (pm20) cc_final: 0.8946 (pm20) REVERT: F 42 GLN cc_start: 0.8120 (mt0) cc_final: 0.7813 (mp10) REVERT: F 54 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: F 70 GLN cc_start: 0.8733 (mm110) cc_final: 0.8454 (mm110) REVERT: F 101 GLN cc_start: 0.7874 (pm20) cc_final: 0.7617 (pm20) REVERT: F 104 LYS cc_start: 0.8602 (tppt) cc_final: 0.8035 (tptt) REVERT: M 113 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.7976 (p0) REVERT: M 119 GLU cc_start: 0.9004 (mp0) cc_final: 0.8240 (mp0) REVERT: M 362 MET cc_start: 0.7995 (ptp) cc_final: 0.7624 (ptm) REVERT: G 10 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8288 (mm-30) REVERT: G 23 LYS cc_start: 0.9242 (tptm) cc_final: 0.8915 (tptp) REVERT: G 65 GLN cc_start: 0.8052 (tt0) cc_final: 0.7691 (mt0) REVERT: G 81 MET cc_start: 0.9313 (ttp) cc_final: 0.9046 (tmm) REVERT: G 82 GLU cc_start: 0.8595 (tt0) cc_final: 0.7928 (tm-30) REVERT: I 42 GLN cc_start: 0.8129 (mt0) cc_final: 0.7810 (mp10) REVERT: I 54 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: I 70 GLN cc_start: 0.8774 (mt0) cc_final: 0.8373 (mm110) REVERT: I 101 GLN cc_start: 0.7902 (pm20) cc_final: 0.7642 (pm20) REVERT: N 113 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.7964 (p0) REVERT: N 119 GLU cc_start: 0.9004 (mp0) cc_final: 0.8224 (mp0) REVERT: N 362 MET cc_start: 0.8003 (ptp) cc_final: 0.7640 (ptm) REVERT: H 10 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8297 (mm-30) REVERT: H 23 LYS cc_start: 0.9230 (tptm) cc_final: 0.8900 (tptp) REVERT: H 46 GLU cc_start: 0.8595 (tt0) cc_final: 0.8337 (tt0) REVERT: H 65 GLN cc_start: 0.8035 (tt0) cc_final: 0.7724 (mt0) REVERT: H 81 MET cc_start: 0.9294 (ttp) cc_final: 0.9027 (tmm) REVERT: H 82 GLU cc_start: 0.8584 (tt0) cc_final: 0.7918 (tm-30) REVERT: L 42 GLN cc_start: 0.8159 (mt0) cc_final: 0.7830 (mp10) REVERT: L 54 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7812 (mtm-85) REVERT: L 70 GLN cc_start: 0.8681 (mm110) cc_final: 0.8352 (mm110) REVERT: L 101 GLN cc_start: 0.7920 (pm20) cc_final: 0.7656 (pm20) REVERT: O 113 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.7961 (p0) REVERT: O 119 GLU cc_start: 0.9006 (mp0) cc_final: 0.8227 (mp0) REVERT: O 362 MET cc_start: 0.8010 (ptp) cc_final: 0.7639 (ptm) REVERT: J 10 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mm-30) REVERT: J 23 LYS cc_start: 0.9244 (tptm) cc_final: 0.8920 (tptp) REVERT: J 65 GLN cc_start: 0.8036 (tt0) cc_final: 0.7681 (mt0) REVERT: J 81 MET cc_start: 0.9310 (ttp) cc_final: 0.9042 (tmm) REVERT: J 82 GLU cc_start: 0.8596 (tt0) cc_final: 0.7928 (tm-30) REVERT: K 42 GLN cc_start: 0.8141 (mt0) cc_final: 0.7814 (mp10) REVERT: K 54 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: K 70 GLN cc_start: 0.8702 (mm110) cc_final: 0.8376 (mm110) REVERT: K 101 GLN cc_start: 0.7898 (pm20) cc_final: 0.7629 (pm20) REVERT: P 113 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.7914 (p0) REVERT: P 119 GLU cc_start: 0.9045 (mp0) cc_final: 0.8271 (mp0) REVERT: P 362 MET cc_start: 0.7992 (ptp) cc_final: 0.7629 (ptm) outliers start: 35 outliers final: 26 residues processed: 377 average time/residue: 0.1457 time to fit residues: 81.9997 Evaluate side-chains 376 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 346 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 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 113 ASP Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 391 GLN N 347 HIS O 347 HIS O 391 GLN P 347 HIS P 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046203 restraints weight = 62712.909| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.73 r_work: 0.2605 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21029 Z= 0.335 Angle : 0.741 9.496 28734 Z= 0.368 Chirality : 0.046 0.177 3354 Planarity : 0.004 0.034 3526 Dihedral : 5.552 20.322 2726 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 2.68 % Allowed : 12.17 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2477 helix: -1.05 (0.97), residues: 28 sheet: -0.35 (0.17), residues: 913 loop : -0.31 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 87 TYR 0.015 0.002 TYR H 80 PHE 0.016 0.002 PHE M 132 TRP 0.012 0.002 TRP E 36 HIS 0.005 0.001 HIS M 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.34 (20899) covalent geometry : angle 0.71734 / 0.36 (28388) SS BOND : bond 0.00425 / 0.27 ( 44) SS BOND : angle 0.51714 / 0.33 ( 88) hydrogen bonds : bond 0.03899 / 2.61 ( 643) hydrogen bonds : angle 6.58432 / 4.64 ( 1632) link_ALPHA1-2 : bond 0.00237 / 0.11 ( 4) link_ALPHA1-2 : angle 2.09391 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00262 / 0.14 ( 8) link_ALPHA1-3 : angle 2.18429 / 1.33 ( 24) link_ALPHA1-6 : bond 0.00268 / 0.12 ( 10) link_ALPHA1-6 : angle 1.69688 / 0.99 ( 30) link_BETA1-4 : bond 0.00325 / 0.20 ( 40) link_BETA1-4 : angle 1.87383 / 1.27 ( 120) link_NAG-ASN : bond 0.00680 / 0.39 ( 24) link_NAG-ASN : angle 2.53588 / 1.66 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.9222 (tptm) cc_final: 0.8920 (tptp) REVERT: E 65 GLN cc_start: 0.8595 (tt0) cc_final: 0.8042 (mt0) REVERT: E 81 MET cc_start: 0.9465 (ttp) cc_final: 0.9013 (tmm) REVERT: E 82 GLU cc_start: 0.8696 (tt0) cc_final: 0.7957 (tm-30) REVERT: F 4 MET cc_start: 0.9038 (tpp) cc_final: 0.8573 (tpp) REVERT: F 27 ARG cc_start: 0.8950 (ptt90) cc_final: 0.8740 (ptt90) REVERT: F 42 GLN cc_start: 0.8409 (mt0) cc_final: 0.7922 (mp10) REVERT: F 70 GLN cc_start: 0.8696 (mm110) cc_final: 0.8396 (mm110) REVERT: F 101 GLN cc_start: 0.8081 (pm20) cc_final: 0.7755 (pm20) REVERT: M 113 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8040 (p0) REVERT: M 119 GLU cc_start: 0.9061 (mp0) cc_final: 0.8376 (mp0) REVERT: M 362 MET cc_start: 0.8185 (ptp) cc_final: 0.7833 (ptm) REVERT: G 10 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8333 (mm-30) REVERT: G 23 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8972 (tptp) REVERT: G 63 LYS cc_start: 0.9580 (mtpp) cc_final: 0.9317 (ptpp) REVERT: G 65 GLN cc_start: 0.8249 (tt0) cc_final: 0.7890 (mt0) REVERT: G 81 MET cc_start: 0.9396 (ttp) cc_final: 0.9050 (tmm) REVERT: G 82 GLU cc_start: 0.8683 (tt0) cc_final: 0.8041 (tm-30) REVERT: I 4 MET cc_start: 0.9044 (tpp) cc_final: 0.8556 (tpp) REVERT: I 27 ARG cc_start: 0.8949 (ptt90) cc_final: 0.8741 (ptt90) REVERT: I 42 GLN cc_start: 0.8391 (mt0) cc_final: 0.7952 (mp10) REVERT: I 70 GLN cc_start: 0.8813 (mt0) cc_final: 0.8423 (mm110) REVERT: I 101 GLN cc_start: 0.8074 (pm20) cc_final: 0.7763 (pm20) REVERT: I 104 LYS cc_start: 0.8957 (tptp) cc_final: 0.8705 (tptp) REVERT: N 113 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8030 (p0) REVERT: N 119 GLU cc_start: 0.9077 (mp0) cc_final: 0.8401 (mp0) REVERT: N 362 MET cc_start: 0.8206 (ptp) cc_final: 0.7870 (ptm) REVERT: H 10 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8336 (mm-30) REVERT: H 23 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8991 (tptp) REVERT: H 46 GLU cc_start: 0.8622 (tt0) cc_final: 0.8279 (tt0) REVERT: H 65 GLN cc_start: 0.8249 (tt0) cc_final: 0.7910 (mt0) REVERT: H 81 MET cc_start: 0.9392 (ttp) cc_final: 0.9041 (tmm) REVERT: H 82 GLU cc_start: 0.8683 (tt0) cc_final: 0.8036 (tm-30) REVERT: L 4 MET cc_start: 0.9034 (tpp) cc_final: 0.8572 (tpp) REVERT: L 27 ARG cc_start: 0.8952 (ptt90) cc_final: 0.8731 (ptt90) REVERT: L 42 GLN cc_start: 0.8405 (mt0) cc_final: 0.7963 (mp10) REVERT: L 70 GLN cc_start: 0.8800 (mm110) cc_final: 0.8463 (mm110) REVERT: L 101 GLN cc_start: 0.8102 (pm20) cc_final: 0.7790 (pm20) REVERT: O 113 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8048 (p0) REVERT: O 119 GLU cc_start: 0.9074 (mp0) cc_final: 0.8403 (mp0) REVERT: O 362 MET cc_start: 0.8201 (ptp) cc_final: 0.7859 (ptm) REVERT: J 10 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8299 (mm-30) REVERT: J 23 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8970 (tptp) REVERT: J 63 LYS cc_start: 0.9578 (mtpp) cc_final: 0.9345 (ptpp) REVERT: J 65 GLN cc_start: 0.8257 (tt0) cc_final: 0.7891 (mt0) REVERT: J 81 MET cc_start: 0.9393 (ttp) cc_final: 0.9051 (tmm) REVERT: J 82 GLU cc_start: 0.8690 (tt0) cc_final: 0.7987 (tm-30) REVERT: K 4 MET cc_start: 0.9071 (tpp) cc_final: 0.8582 (tpp) REVERT: K 27 ARG cc_start: 0.8973 (ptt90) cc_final: 0.8756 (ptt90) REVERT: K 42 GLN cc_start: 0.8407 (mt0) cc_final: 0.7964 (mp10) REVERT: K 70 GLN cc_start: 0.8781 (mm110) cc_final: 0.8471 (mm110) REVERT: K 101 GLN cc_start: 0.8103 (pm20) cc_final: 0.7783 (pm20) REVERT: P 113 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8104 (p0) REVERT: P 119 GLU cc_start: 0.9071 (mp0) cc_final: 0.8392 (mp0) REVERT: P 362 MET cc_start: 0.8189 (ptp) cc_final: 0.7850 (ptm) outliers start: 57 outliers final: 43 residues processed: 372 average time/residue: 0.1421 time to fit residues: 79.9438 Evaluate side-chains 378 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 328 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 228 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 11 VAL Chi-restraints excluded: chain G residue 23 LYS 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 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 219 optimal weight: 0.0970 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 391 GLN P 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051971 restraints weight = 60138.774| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.77 r_work: 0.2691 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21029 Z= 0.116 Angle : 0.627 8.133 28734 Z= 0.315 Chirality : 0.043 0.179 3354 Planarity : 0.004 0.037 3526 Dihedral : 5.132 19.067 2726 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 2.16 % Allowed : 13.01 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2477 helix: -1.59 (0.81), residues: 28 sheet: -0.30 (0.17), residues: 938 loop : -0.05 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 19 TYR 0.015 0.001 TYR E 80 PHE 0.016 0.001 PHE L 83 TRP 0.016 0.001 TRP P 178 HIS 0.003 0.001 HIS P 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (20899) covalent geometry : angle 0.61327 / 0.31 (28388) SS BOND : bond 0.00200 / 0.11 ( 44) SS BOND : angle 0.43573 / 0.26 ( 88) hydrogen bonds : bond 0.03358 / 2.20 ( 643) hydrogen bonds : angle 6.32614 / 4.45 ( 1632) link_ALPHA1-2 : bond 0.00868 / 0.41 ( 4) link_ALPHA1-2 : angle 1.91907 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00738 / 0.35 ( 8) link_ALPHA1-3 : angle 1.31295 / 0.82 ( 24) link_ALPHA1-6 : bond 0.00491 / 0.26 ( 10) link_ALPHA1-6 : angle 1.40516 / 0.84 ( 30) link_BETA1-4 : bond 0.00439 / 0.26 ( 40) link_BETA1-4 : angle 1.39911 / 0.96 ( 120) link_NAG-ASN : bond 0.00104 / 0.05 ( 24) link_NAG-ASN : angle 1.78847 / 1.15 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8334 (mm-30) REVERT: E 23 LYS cc_start: 0.9204 (tptm) cc_final: 0.8903 (tptp) REVERT: E 65 GLN cc_start: 0.8545 (tt0) cc_final: 0.8027 (mt0) REVERT: E 81 MET cc_start: 0.9355 (ttp) cc_final: 0.9036 (tmm) REVERT: E 82 GLU cc_start: 0.8680 (tt0) cc_final: 0.7988 (tm-30) REVERT: F 42 GLN cc_start: 0.8305 (mt0) cc_final: 0.7848 (mp10) REVERT: F 70 GLN cc_start: 0.8728 (mm110) cc_final: 0.8470 (mm110) REVERT: F 101 GLN cc_start: 0.8054 (pm20) cc_final: 0.7778 (pm20) REVERT: F 104 LYS cc_start: 0.8855 (tptt) cc_final: 0.8147 (tptt) REVERT: M 113 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8080 (p0) REVERT: M 119 GLU cc_start: 0.8998 (mp0) cc_final: 0.8777 (mp0) REVERT: M 362 MET cc_start: 0.7939 (ptp) cc_final: 0.7610 (ptm) REVERT: G 10 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8531 (mm-30) REVERT: G 23 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8962 (tptp) REVERT: G 65 GLN cc_start: 0.8133 (tt0) cc_final: 0.7847 (mt0) REVERT: G 81 MET cc_start: 0.9308 (ttp) cc_final: 0.9032 (tmm) REVERT: G 82 GLU cc_start: 0.8635 (tt0) cc_final: 0.8041 (tm-30) REVERT: I 42 GLN cc_start: 0.8250 (mt0) cc_final: 0.7901 (mp10) REVERT: I 70 GLN cc_start: 0.8853 (mt0) cc_final: 0.8567 (mm110) REVERT: I 101 GLN cc_start: 0.8022 (pm20) cc_final: 0.7755 (pm20) REVERT: I 104 LYS cc_start: 0.8775 (tptp) cc_final: 0.8284 (tptp) REVERT: N 113 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8073 (p0) REVERT: N 119 GLU cc_start: 0.8995 (mp0) cc_final: 0.8778 (mp0) REVERT: H 10 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8536 (mm-30) REVERT: H 23 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8942 (tptp) REVERT: H 46 GLU cc_start: 0.8703 (tt0) cc_final: 0.8345 (tt0) REVERT: H 65 GLN cc_start: 0.8183 (tt0) cc_final: 0.7951 (mt0) REVERT: H 81 MET cc_start: 0.9295 (ttp) cc_final: 0.8871 (tmm) REVERT: H 82 GLU cc_start: 0.8639 (tt0) cc_final: 0.8081 (tm-30) REVERT: L 42 GLN cc_start: 0.8244 (mt0) cc_final: 0.7890 (mp10) REVERT: L 70 GLN cc_start: 0.8779 (mm110) cc_final: 0.8538 (mm110) REVERT: L 101 GLN cc_start: 0.8017 (pm20) cc_final: 0.7752 (pm20) REVERT: O 113 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8086 (p0) REVERT: O 119 GLU cc_start: 0.9003 (mp0) cc_final: 0.8789 (mp0) REVERT: O 362 MET cc_start: 0.7942 (ptp) cc_final: 0.7741 (ptm) REVERT: J 10 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8490 (mm-30) REVERT: J 23 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8967 (tptp) REVERT: J 65 GLN cc_start: 0.8127 (tt0) cc_final: 0.7834 (mt0) REVERT: J 81 MET cc_start: 0.9304 (ttp) cc_final: 0.9008 (tmm) REVERT: J 82 GLU cc_start: 0.8653 (tt0) cc_final: 0.8016 (tm-30) REVERT: K 42 GLN cc_start: 0.8267 (mt0) cc_final: 0.7913 (mp10) REVERT: K 70 GLN cc_start: 0.8788 (mm110) cc_final: 0.8511 (mm110) REVERT: K 101 GLN cc_start: 0.8019 (pm20) cc_final: 0.7724 (pm20) REVERT: P 113 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8152 (p0) REVERT: P 119 GLU cc_start: 0.9010 (mp0) cc_final: 0.8789 (mp0) REVERT: P 362 MET cc_start: 0.7931 (ptp) cc_final: 0.7611 (ptm) outliers start: 46 outliers final: 35 residues processed: 369 average time/residue: 0.1398 time to fit residues: 78.7289 Evaluate side-chains 379 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 188 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 65 GLN H 65 GLN O 391 GLN J 65 GLN P 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.046343 restraints weight = 62916.189| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.74 r_work: 0.2607 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 21029 Z= 0.349 Angle : 0.733 9.644 28734 Z= 0.365 Chirality : 0.046 0.178 3354 Planarity : 0.004 0.049 3526 Dihedral : 5.370 21.570 2726 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer: Outliers : 2.35 % Allowed : 13.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2477 helix: -0.89 (0.99), residues: 28 sheet: -0.34 (0.17), residues: 914 loop : -0.27 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.015 0.002 TYR E 80 PHE 0.033 0.002 PHE I 83 TRP 0.012 0.002 TRP I 35 HIS 0.005 0.001 HIS N 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.35 (20899) covalent geometry : angle 0.71220 / 0.36 (28388) SS BOND : bond 0.00437 / 0.28 ( 44) SS BOND : angle 0.48955 / 0.32 ( 88) hydrogen bonds : bond 0.03797 / 2.53 ( 643) hydrogen bonds : angle 6.47739 / 4.57 ( 1632) link_ALPHA1-2 : bond 0.00244 / 0.11 ( 4) link_ALPHA1-2 : angle 2.03436 / 1.01 ( 12) link_ALPHA1-3 : bond 0.00266 / 0.15 ( 8) link_ALPHA1-3 : angle 2.15917 / 1.32 ( 24) link_ALPHA1-6 : bond 0.00266 / 0.12 ( 10) link_ALPHA1-6 : angle 1.66555 / 0.97 ( 30) link_BETA1-4 : bond 0.00296 / 0.18 ( 40) link_BETA1-4 : angle 1.73451 / 1.18 ( 120) link_NAG-ASN : bond 0.00692 / 0.39 ( 24) link_NAG-ASN : angle 2.40374 / 1.57 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8356 (mm-30) REVERT: E 23 LYS cc_start: 0.9170 (tptm) cc_final: 0.8840 (tptp) REVERT: E 65 GLN cc_start: 0.8732 (tt0) cc_final: 0.8198 (mt0) REVERT: E 81 MET cc_start: 0.9465 (ttp) cc_final: 0.8960 (tmm) REVERT: E 82 GLU cc_start: 0.8700 (tt0) cc_final: 0.7985 (tm-30) REVERT: E 102 ASP cc_start: 0.8609 (p0) cc_final: 0.8397 (p0) REVERT: F 42 GLN cc_start: 0.8399 (mt0) cc_final: 0.7898 (mp10) REVERT: F 70 GLN cc_start: 0.8688 (mm110) cc_final: 0.8416 (mm110) REVERT: F 101 GLN cc_start: 0.8091 (pm20) cc_final: 0.7790 (pm20) REVERT: F 104 LYS cc_start: 0.8522 (tptt) cc_final: 0.8295 (tptt) REVERT: M 113 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8156 (p0) REVERT: M 119 GLU cc_start: 0.9030 (mp0) cc_final: 0.8321 (mp0) REVERT: M 362 MET cc_start: 0.8031 (ptp) cc_final: 0.7706 (ptm) REVERT: G 10 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8386 (mm-30) REVERT: G 23 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8891 (tptp) REVERT: G 65 GLN cc_start: 0.8262 (tt0) cc_final: 0.7621 (mt0) REVERT: G 81 MET cc_start: 0.9410 (ttp) cc_final: 0.8984 (tmm) REVERT: G 82 GLU cc_start: 0.8661 (tt0) cc_final: 0.8006 (tm-30) REVERT: I 4 MET cc_start: 0.9025 (tpp) cc_final: 0.8544 (tpp) REVERT: I 42 GLN cc_start: 0.8347 (mt0) cc_final: 0.7889 (mp10) REVERT: I 70 GLN cc_start: 0.8827 (mt0) cc_final: 0.8507 (mm110) REVERT: I 101 GLN cc_start: 0.8071 (pm20) cc_final: 0.7770 (pm20) REVERT: N 113 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8454 (p0) REVERT: N 119 GLU cc_start: 0.9039 (mp0) cc_final: 0.8342 (mp0) REVERT: H 10 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8393 (mm-30) REVERT: H 23 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: H 46 GLU cc_start: 0.8675 (tt0) cc_final: 0.8306 (tt0) REVERT: H 65 GLN cc_start: 0.8231 (tt0) cc_final: 0.7941 (mt0) REVERT: H 81 MET cc_start: 0.9410 (ttp) cc_final: 0.8992 (tmm) REVERT: H 82 GLU cc_start: 0.8661 (tt0) cc_final: 0.7998 (tm-30) REVERT: L 4 MET cc_start: 0.8997 (tpp) cc_final: 0.8573 (tpp) REVERT: L 27 ARG cc_start: 0.8949 (ptt90) cc_final: 0.8582 (ptt180) REVERT: L 42 GLN cc_start: 0.8351 (mt0) cc_final: 0.7941 (mp10) REVERT: L 70 GLN cc_start: 0.8711 (mm110) cc_final: 0.8435 (mm110) REVERT: L 101 GLN cc_start: 0.8099 (pm20) cc_final: 0.7797 (pm20) REVERT: O 113 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8161 (p0) REVERT: O 119 GLU cc_start: 0.9040 (mp0) cc_final: 0.8351 (mp0) REVERT: O 362 MET cc_start: 0.8030 (ptp) cc_final: 0.7713 (ptm) REVERT: J 10 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8487 (mm-30) REVERT: J 23 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8899 (tptp) REVERT: J 65 GLN cc_start: 0.8278 (tt0) cc_final: 0.7644 (mt0) REVERT: J 81 MET cc_start: 0.9430 (ttp) cc_final: 0.8961 (tmm) REVERT: J 82 GLU cc_start: 0.8665 (tt0) cc_final: 0.7997 (tm-30) REVERT: K 4 MET cc_start: 0.9009 (tpp) cc_final: 0.8545 (tpp) REVERT: K 27 ARG cc_start: 0.8955 (ptt90) cc_final: 0.8595 (ptt180) REVERT: K 42 GLN cc_start: 0.8353 (mt0) cc_final: 0.7908 (mp10) REVERT: K 70 GLN cc_start: 0.8741 (mm110) cc_final: 0.8436 (mm110) REVERT: K 81 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8419 (tm-30) REVERT: K 101 GLN cc_start: 0.8035 (pm20) cc_final: 0.7724 (pm20) REVERT: P 113 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8187 (p0) REVERT: P 119 GLU cc_start: 0.9034 (mp0) cc_final: 0.8332 (mp0) REVERT: P 362 MET cc_start: 0.8016 (ptp) cc_final: 0.7704 (ptm) outliers start: 50 outliers final: 35 residues processed: 352 average time/residue: 0.1449 time to fit residues: 77.3231 Evaluate side-chains 359 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain M residue 113 ASP 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 G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN G 62 GLN J 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050489 restraints weight = 61932.056| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.86 r_work: 0.2639 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21029 Z= 0.200 Angle : 0.678 8.553 28734 Z= 0.339 Chirality : 0.043 0.153 3354 Planarity : 0.004 0.042 3526 Dihedral : 5.274 25.394 2726 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 2.87 % Allowed : 13.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2477 helix: -1.05 (0.92), residues: 28 sheet: -0.26 (0.17), residues: 958 loop : -0.16 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 87 TYR 0.012 0.001 TYR E 80 PHE 0.031 0.002 PHE I 83 TRP 0.013 0.001 TRP P 178 HIS 0.003 0.001 HIS O 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (20899) covalent geometry : angle 0.66238 / 0.34 (28388) SS BOND : bond 0.00271 / 0.17 ( 44) SS BOND : angle 0.40842 / 0.25 ( 88) hydrogen bonds : bond 0.03538 / 2.33 ( 643) hydrogen bonds : angle 6.35769 / 4.48 ( 1632) link_ALPHA1-2 : bond 0.00568 / 0.27 ( 4) link_ALPHA1-2 : angle 2.02032 / 1.02 ( 12) link_ALPHA1-3 : bond 0.00344 / 0.16 ( 8) link_ALPHA1-3 : angle 1.64015 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00317 / 0.15 ( 10) link_ALPHA1-6 : angle 1.53265 / 0.90 ( 30) link_BETA1-4 : bond 0.00315 / 0.19 ( 40) link_BETA1-4 : angle 1.48033 / 1.02 ( 120) link_NAG-ASN : bond 0.00326 / 0.18 ( 24) link_NAG-ASN : angle 2.04075 / 1.32 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 336 time to evaluate : 0.604 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: 0.8672 (mm-30) cc_final: 0.8394 (mm-30) REVERT: E 23 LYS cc_start: 0.9183 (tptm) cc_final: 0.8851 (tptp) REVERT: E 63 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9277 (ptpp) REVERT: E 65 GLN cc_start: 0.8749 (tt0) cc_final: 0.8194 (mt0) REVERT: E 81 MET cc_start: 0.9364 (ttp) cc_final: 0.9012 (tmm) REVERT: E 82 GLU cc_start: 0.8728 (tt0) cc_final: 0.8000 (tm-30) REVERT: F 4 MET cc_start: 0.9059 (tpp) cc_final: 0.8606 (tpp) REVERT: F 42 GLN cc_start: 0.8411 (mt0) cc_final: 0.7914 (mp10) REVERT: F 70 GLN cc_start: 0.8704 (mm110) cc_final: 0.8386 (mm110) REVERT: F 101 GLN cc_start: 0.8105 (pm20) cc_final: 0.7787 (pm20) REVERT: M 113 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8150 (p0) REVERT: M 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.8323 (mp0) REVERT: M 362 MET cc_start: 0.7986 (ptp) cc_final: 0.7655 (ptm) REVERT: G 10 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8491 (mm-30) REVERT: G 23 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8947 (tptp) REVERT: G 63 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9265 (ptpp) REVERT: G 65 GLN cc_start: 0.8272 (tt0) cc_final: 0.7605 (mt0) REVERT: G 81 MET cc_start: 0.9355 (ttp) cc_final: 0.8909 (tmm) REVERT: G 82 GLU cc_start: 0.8680 (tt0) cc_final: 0.8097 (tm-30) REVERT: G 112 ASP cc_start: 0.8573 (m-30) cc_final: 0.8369 (m-30) REVERT: I 4 MET cc_start: 0.9062 (tpp) cc_final: 0.8613 (tpp) REVERT: I 42 GLN cc_start: 0.8356 (mt0) cc_final: 0.7914 (mp10) REVERT: I 70 GLN cc_start: 0.8844 (mt0) cc_final: 0.8533 (mm110) REVERT: I 101 GLN cc_start: 0.8121 (pm20) cc_final: 0.7801 (pm20) REVERT: N 113 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8153 (p0) REVERT: N 119 GLU cc_start: 0.9053 (mp0) cc_final: 0.8822 (mp0) REVERT: H 10 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8505 (mm-30) REVERT: H 23 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8915 (tptp) REVERT: H 46 GLU cc_start: 0.8732 (tt0) cc_final: 0.8357 (tt0) REVERT: H 65 GLN cc_start: 0.8230 (tt0) cc_final: 0.7946 (mt0) REVERT: H 81 MET cc_start: 0.9409 (ttp) cc_final: 0.8857 (tmm) REVERT: H 82 GLU cc_start: 0.8680 (tt0) cc_final: 0.8083 (tm-30) REVERT: H 112 ASP cc_start: 0.8542 (m-30) cc_final: 0.8338 (m-30) REVERT: L 42 GLN cc_start: 0.8343 (mt0) cc_final: 0.7944 (mp10) REVERT: L 70 GLN cc_start: 0.8763 (mm110) cc_final: 0.8500 (mm110) REVERT: L 101 GLN cc_start: 0.8096 (pm20) cc_final: 0.7788 (pm20) REVERT: O 113 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8166 (p0) REVERT: O 119 GLU cc_start: 0.9060 (mp0) cc_final: 0.8838 (mp0) REVERT: O 362 MET cc_start: 0.7985 (ptp) cc_final: 0.7663 (ptm) REVERT: J 10 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8510 (mm-30) REVERT: J 23 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8948 (tptp) REVERT: J 46 GLU cc_start: 0.8283 (tt0) cc_final: 0.8075 (tt0) REVERT: J 63 LYS cc_start: 0.9477 (ptpp) cc_final: 0.9253 (ptpp) REVERT: J 65 GLN cc_start: 0.8287 (tt0) cc_final: 0.7614 (mt0) REVERT: J 81 MET cc_start: 0.9355 (ttp) cc_final: 0.9029 (tmm) REVERT: J 82 GLU cc_start: 0.8686 (tt0) cc_final: 0.8008 (tm-30) REVERT: J 112 ASP cc_start: 0.8564 (m-30) cc_final: 0.8364 (m-30) REVERT: K 4 MET cc_start: 0.9068 (tpp) cc_final: 0.8645 (tpp) REVERT: K 42 GLN cc_start: 0.8356 (mt0) cc_final: 0.7960 (mp10) REVERT: K 70 GLN cc_start: 0.8777 (mm110) cc_final: 0.8443 (mm110) REVERT: K 81 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8369 (tm-30) REVERT: K 101 GLN cc_start: 0.8033 (pm20) cc_final: 0.7729 (pm20) REVERT: P 113 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8185 (p0) REVERT: P 119 GLU cc_start: 0.9027 (mp0) cc_final: 0.8341 (mp0) REVERT: P 362 MET cc_start: 0.7965 (ptp) cc_final: 0.7663 (ptm) outliers start: 61 outliers final: 41 residues processed: 367 average time/residue: 0.1472 time to fit residues: 82.1287 Evaluate side-chains 365 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 169 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN J 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.047079 restraints weight = 62200.239| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.77 r_work: 0.2629 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21029 Z= 0.236 Angle : 0.698 8.981 28734 Z= 0.349 Chirality : 0.044 0.154 3354 Planarity : 0.004 0.053 3526 Dihedral : 5.399 31.840 2726 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 2.63 % Allowed : 14.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2477 helix: -0.79 (0.98), residues: 28 sheet: -0.27 (0.17), residues: 921 loop : -0.17 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 87 TYR 0.011 0.001 TYR M 121 PHE 0.028 0.002 PHE I 83 TRP 0.011 0.001 TRP P 178 HIS 0.003 0.001 HIS O 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (20899) covalent geometry : angle 0.68133 / 0.35 (28388) SS BOND : bond 0.00305 / 0.19 ( 44) SS BOND : angle 0.41811 / 0.26 ( 88) hydrogen bonds : bond 0.03631 / 2.41 ( 643) hydrogen bonds : angle 6.39697 / 4.50 ( 1632) link_ALPHA1-2 : bond 0.00349 / 0.16 ( 4) link_ALPHA1-2 : angle 1.99834 / 1.00 ( 12) link_ALPHA1-3 : bond 0.00205 / 0.10 ( 8) link_ALPHA1-3 : angle 1.80503 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00273 / 0.13 ( 10) link_ALPHA1-6 : angle 1.58809 / 0.93 ( 30) link_BETA1-4 : bond 0.00267 / 0.16 ( 40) link_BETA1-4 : angle 1.51859 / 1.04 ( 120) link_NAG-ASN : bond 0.00445 / 0.25 ( 24) link_NAG-ASN : angle 2.13541 / 1.38 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8376 (mm-30) REVERT: E 23 LYS cc_start: 0.9195 (tptm) cc_final: 0.8853 (tptp) REVERT: E 65 GLN cc_start: 0.8778 (tt0) cc_final: 0.8176 (mt0) REVERT: E 81 MET cc_start: 0.9406 (ttp) cc_final: 0.9050 (tmm) REVERT: E 82 GLU cc_start: 0.8760 (tt0) cc_final: 0.8074 (tm-30) REVERT: F 4 MET cc_start: 0.9035 (tpp) cc_final: 0.8628 (tpp) REVERT: F 42 GLN cc_start: 0.8431 (mt0) cc_final: 0.7945 (mp10) REVERT: F 70 GLN cc_start: 0.8722 (mm110) cc_final: 0.8403 (mm110) REVERT: F 101 GLN cc_start: 0.8095 (pm20) cc_final: 0.7763 (pm20) REVERT: F 104 LYS cc_start: 0.8745 (tptt) cc_final: 0.8146 (tptp) REVERT: M 113 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8157 (p0) REVERT: M 119 GLU cc_start: 0.9041 (mp0) cc_final: 0.8338 (mp0) REVERT: M 362 MET cc_start: 0.8048 (ptp) cc_final: 0.7720 (ptm) REVERT: G 10 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30) REVERT: G 23 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8939 (tptp) REVERT: G 63 LYS cc_start: 0.9485 (ptpp) cc_final: 0.9280 (ptpp) REVERT: G 65 GLN cc_start: 0.8288 (tt0) cc_final: 0.7583 (mt0) REVERT: G 81 MET cc_start: 0.9392 (ttp) cc_final: 0.9032 (tmm) REVERT: G 82 GLU cc_start: 0.8749 (tt0) cc_final: 0.8064 (tm-30) REVERT: I 4 MET cc_start: 0.9072 (tpp) cc_final: 0.8676 (tpp) REVERT: I 24 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8185 (mtp85) REVERT: I 42 GLN cc_start: 0.8419 (mt0) cc_final: 0.7971 (mp10) REVERT: I 70 GLN cc_start: 0.8871 (mt0) cc_final: 0.8557 (mm110) REVERT: I 101 GLN cc_start: 0.8106 (pm20) cc_final: 0.7775 (pm20) REVERT: N 113 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8165 (p0) REVERT: N 119 GLU cc_start: 0.9053 (mp0) cc_final: 0.8383 (mp0) REVERT: H 10 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8538 (mm-30) REVERT: H 23 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8931 (tptp) REVERT: H 46 GLU cc_start: 0.8758 (tt0) cc_final: 0.8378 (tt0) REVERT: H 65 GLN cc_start: 0.8267 (tt0) cc_final: 0.7942 (mt0) REVERT: H 81 MET cc_start: 0.9444 (ttp) cc_final: 0.8855 (tmm) REVERT: H 82 GLU cc_start: 0.8749 (tt0) cc_final: 0.8101 (tm-30) REVERT: L 4 MET cc_start: 0.9063 (tpp) cc_final: 0.8680 (tpp) REVERT: L 42 GLN cc_start: 0.8370 (mt0) cc_final: 0.7922 (mp10) REVERT: L 70 GLN cc_start: 0.8774 (mm110) cc_final: 0.8512 (mm110) REVERT: L 101 GLN cc_start: 0.8100 (pm20) cc_final: 0.7783 (pm20) REVERT: O 113 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8178 (p0) REVERT: O 119 GLU cc_start: 0.9060 (mp0) cc_final: 0.8396 (mp0) REVERT: O 362 MET cc_start: 0.8048 (ptp) cc_final: 0.7717 (ptm) REVERT: J 10 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8517 (mm-30) REVERT: J 23 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8940 (tptp) REVERT: J 46 GLU cc_start: 0.8319 (tt0) cc_final: 0.8098 (tt0) REVERT: J 63 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9275 (ptpp) REVERT: J 65 GLN cc_start: 0.8327 (tt0) cc_final: 0.7614 (mt0) REVERT: J 81 MET cc_start: 0.9389 (ttp) cc_final: 0.9037 (tmm) REVERT: J 82 GLU cc_start: 0.8748 (tt0) cc_final: 0.8071 (tm-30) REVERT: K 42 GLN cc_start: 0.8412 (mt0) cc_final: 0.7969 (mp10) REVERT: K 70 GLN cc_start: 0.8794 (mm110) cc_final: 0.8461 (mm110) REVERT: K 101 GLN cc_start: 0.8040 (pm20) cc_final: 0.7732 (pm20) REVERT: P 113 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8196 (p0) REVERT: P 119 GLU cc_start: 0.9036 (mp0) cc_final: 0.8356 (mp0) REVERT: P 362 MET cc_start: 0.8031 (ptp) cc_final: 0.7704 (ptm) outliers start: 56 outliers final: 45 residues processed: 355 average time/residue: 0.1476 time to fit residues: 80.2778 Evaluate side-chains 367 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 427 ILE Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.046998 restraints weight = 62771.318| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.83 r_work: 0.2629 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 21029 Z= 0.303 Angle : 0.936 59.199 28734 Z= 0.524 Chirality : 0.044 0.249 3354 Planarity : 0.004 0.052 3526 Dihedral : 5.389 31.137 2726 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 2.58 % Allowed : 14.61 % Favored : 82.81 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2477 helix: -0.79 (0.98), residues: 28 sheet: -0.27 (0.17), residues: 921 loop : -0.16 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 87 TYR 0.011 0.002 TYR M 121 PHE 0.033 0.002 PHE F 83 TRP 0.011 0.001 TRP P 178 HIS 0.002 0.001 HIS O 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.30 (20899) covalent geometry : angle 0.92575 / 0.52 (28388) SS BOND : bond 0.00314 / 0.20 ( 44) SS BOND : angle 0.41038 / 0.26 ( 88) hydrogen bonds : bond 0.03638 / 2.41 ( 643) hydrogen bonds : angle 6.39501 / 4.50 ( 1632) link_ALPHA1-2 : bond 0.00495 / 0.24 ( 4) link_ALPHA1-2 : angle 2.05521 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00183 / 0.09 ( 8) link_ALPHA1-3 : angle 1.80381 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00286 / 0.13 ( 10) link_ALPHA1-6 : angle 1.58930 / 0.93 ( 30) link_BETA1-4 : bond 0.00316 / 0.19 ( 40) link_BETA1-4 : angle 1.54018 / 1.06 ( 120) link_NAG-ASN : bond 0.00448 / 0.25 ( 24) link_NAG-ASN : angle 2.13130 / 1.38 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8365 (mm-30) REVERT: E 23 LYS cc_start: 0.9176 (tptm) cc_final: 0.8836 (tptp) REVERT: E 65 GLN cc_start: 0.8767 (tt0) cc_final: 0.8165 (mt0) REVERT: E 81 MET cc_start: 0.9397 (ttp) cc_final: 0.8982 (tmm) REVERT: E 82 GLU cc_start: 0.8744 (tt0) cc_final: 0.8079 (tm-30) REVERT: F 4 MET cc_start: 0.9017 (tpp) cc_final: 0.8616 (tpp) REVERT: F 42 GLN cc_start: 0.8409 (mt0) cc_final: 0.7927 (mp10) REVERT: F 70 GLN cc_start: 0.8706 (mm110) cc_final: 0.8394 (mm110) REVERT: F 101 GLN cc_start: 0.8059 (pm20) cc_final: 0.7733 (pm20) REVERT: M 113 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8151 (p0) REVERT: M 119 GLU cc_start: 0.9023 (mp0) cc_final: 0.8322 (mp0) REVERT: M 362 MET cc_start: 0.8010 (ptp) cc_final: 0.7686 (ptm) REVERT: G 10 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8507 (mm-30) REVERT: G 23 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: G 65 GLN cc_start: 0.8259 (tt0) cc_final: 0.7482 (mt0) REVERT: G 81 MET cc_start: 0.9402 (ttp) cc_final: 0.9018 (tmm) REVERT: G 82 GLU cc_start: 0.8691 (tt0) cc_final: 0.8037 (tm-30) REVERT: I 4 MET cc_start: 0.9059 (tpp) cc_final: 0.8669 (tpp) REVERT: I 24 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8175 (mtp85) REVERT: I 42 GLN cc_start: 0.8381 (mt0) cc_final: 0.7941 (mp10) REVERT: I 70 GLN cc_start: 0.8839 (mt0) cc_final: 0.8542 (mm110) REVERT: I 101 GLN cc_start: 0.8081 (pm20) cc_final: 0.7750 (pm20) REVERT: N 113 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8157 (p0) REVERT: N 119 GLU cc_start: 0.9053 (mp0) cc_final: 0.8378 (mp0) REVERT: H 10 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8532 (mm-30) REVERT: H 23 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8915 (tptp) REVERT: H 46 GLU cc_start: 0.8740 (tt0) cc_final: 0.8355 (tt0) REVERT: H 65 GLN cc_start: 0.8250 (tt0) cc_final: 0.7926 (mt0) REVERT: H 81 MET cc_start: 0.9446 (ttp) cc_final: 0.8829 (tmm) REVERT: H 82 GLU cc_start: 0.8689 (tt0) cc_final: 0.8070 (tm-30) REVERT: L 4 MET cc_start: 0.9048 (tpp) cc_final: 0.8672 (tpp) REVERT: L 42 GLN cc_start: 0.8338 (mt0) cc_final: 0.7897 (mp10) REVERT: L 70 GLN cc_start: 0.8758 (mm110) cc_final: 0.8499 (mm110) REVERT: L 101 GLN cc_start: 0.8069 (pm20) cc_final: 0.7756 (pm20) REVERT: O 113 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8171 (p0) REVERT: O 119 GLU cc_start: 0.9052 (mp0) cc_final: 0.8380 (mp0) REVERT: O 362 MET cc_start: 0.8002 (ptp) cc_final: 0.7676 (ptm) REVERT: J 10 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8508 (mm-30) REVERT: J 23 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8927 (tptp) REVERT: J 46 GLU cc_start: 0.8283 (tt0) cc_final: 0.8059 (tt0) REVERT: J 65 GLN cc_start: 0.8276 (tt0) cc_final: 0.7489 (mt0) REVERT: J 81 MET cc_start: 0.9386 (ttp) cc_final: 0.9022 (tmm) REVERT: J 82 GLU cc_start: 0.8731 (tt0) cc_final: 0.8070 (tm-30) REVERT: K 42 GLN cc_start: 0.8385 (mt0) cc_final: 0.7946 (mp10) REVERT: K 70 GLN cc_start: 0.8777 (mm110) cc_final: 0.8446 (mm110) REVERT: K 79 GLN cc_start: 0.9218 (mm110) cc_final: 0.8949 (mp10) REVERT: K 101 GLN cc_start: 0.8018 (pm20) cc_final: 0.7711 (pm20) REVERT: P 113 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8188 (p0) REVERT: P 119 GLU cc_start: 0.9023 (mp0) cc_final: 0.8345 (mp0) REVERT: P 362 MET cc_start: 0.7997 (ptp) cc_final: 0.7674 (ptm) outliers start: 55 outliers final: 43 residues processed: 344 average time/residue: 0.1371 time to fit residues: 72.1385 Evaluate side-chains 362 residues out of total 2129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 230 CYS Chi-restraints excluded: chain M residue 444 VAL Chi-restraints excluded: chain M residue 449 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 230 CYS Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 449 THR Chi-restraints excluded: chain N residue 467 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 109 SER Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 230 CYS Chi-restraints excluded: chain O residue 444 VAL Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain O residue 467 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 90 HIS Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 230 CYS Chi-restraints excluded: chain P residue 444 VAL Chi-restraints excluded: chain P residue 449 THR Chi-restraints excluded: chain P residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 41 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.046973 restraints weight = 62741.490| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.83 r_work: 0.2627 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 21029 Z= 0.303 Angle : 0.936 59.199 28734 Z= 0.524 Chirality : 0.044 0.249 3354 Planarity : 0.004 0.052 3526 Dihedral : 5.389 31.137 2726 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 2.35 % Allowed : 14.98 % Favored : 82.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2477 helix: -0.79 (0.98), residues: 28 sheet: -0.27 (0.17), residues: 921 loop : -0.16 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 87 TYR 0.011 0.002 TYR M 121 PHE 0.033 0.002 PHE F 83 TRP 0.011 0.001 TRP P 178 HIS 0.002 0.001 HIS O 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.30 (20899) covalent geometry : angle 0.92575 / 0.52 (28388) SS BOND : bond 0.00314 / 0.20 ( 44) SS BOND : angle 0.41038 / 0.26 ( 88) hydrogen bonds : bond 0.03638 / 2.41 ( 643) hydrogen bonds : angle 6.39501 / 4.50 ( 1632) link_ALPHA1-2 : bond 0.00495 / 0.24 ( 4) link_ALPHA1-2 : angle 2.05521 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00183 / 0.09 ( 8) link_ALPHA1-3 : angle 1.80381 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00286 / 0.13 ( 10) link_ALPHA1-6 : angle 1.58930 / 0.93 ( 30) link_BETA1-4 : bond 0.00316 / 0.19 ( 40) link_BETA1-4 : angle 1.54018 / 1.06 ( 120) link_NAG-ASN : bond 0.00448 / 0.25 ( 24) link_NAG-ASN : angle 2.13130 / 1.38 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4211.73 seconds wall clock time: 73 minutes 36.60 seconds (4416.60 seconds total)