Starting phenix.real_space_refine on Mon May 19 14:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3q_29708/05_2025/8g3q_29708.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 109 5.16 5 C 11520 2.51 5 N 3120 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18618 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" 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: "G" 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: 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: "F" 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: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "D" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.19, per 1000 atoms: 0.65 Number of scatterers: 18618 At special positions: 0 Unit cell: (134.48, 136.12, 119.72, 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 109 16.00 O 3864 8.00 N 3120 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.98 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.08 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.05 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.04 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.07 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.16 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.05 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.06 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.01 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.07 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.06 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.07 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.04 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.12 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=1.99 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.06 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.07 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.08 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.05 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.06 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.07 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=1.99 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.06 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.07 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.07 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.04 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS F 337 " distance=2.08 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 447 " distance=2.14 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 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 c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " 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 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " 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 f 2 " - " BMA f 3 " " 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " 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 t 2 " - " BMA t 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " NAG-ASN " NAG 1 1 " - " ASN H 86 " " NAG 2 1 " - " ASN H 146 " " NAG 3 1 " - " ASN H 200 " " NAG 4 1 " - " ASN H 234 " " NAG 6 1 " - " ASN H 329 " " NAG 7 1 " - " ASN H 367 " " NAG a 1 " - " ASN E 86 " " NAG b 1 " - " ASN E 146 " " NAG c 1 " - " ASN E 200 " " NAG d 1 " - " ASN E 234 " " NAG f 1 " - " ASN E 329 " " NAG g 1 " - " ASN E 367 " " NAG i 1 " - " ASN F 86 " " NAG j 1 " - " ASN F 146 " " NAG k 1 " - " ASN F 200 " " NAG l 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 329 " " NAG o 1 " - " ASN F 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4098 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 42 sheets defined 3.4% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.747A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.835A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.668A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.673A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.021A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.466A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.288A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.381A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.313A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.432A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.071A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.680A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.676A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.040A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.467A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.289A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.384A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.498A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.696A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.674A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.012A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.461A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.308A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.389A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.330A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.441A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.675A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG F 420 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.667A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 172 " --> pdb=" O MET F 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 184 removed outlier: 3.993A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 207 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU F 211 " --> pdb=" O TYR F 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 6.455A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 283 removed outlier: 5.285A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 352 through 356 removed outlier: 4.419A pdb=" N TRP F 352 " --> pdb=" O GLY F 363 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.316A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.484A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.500A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.492A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASN C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.475A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.575A pdb=" N ASN I 117 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.509A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.505A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.550A pdb=" N ASN A 117 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 104 through 105 613 hydrogen bonds defined for protein. 1581 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: 6.89 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3243 1.31 - 1.44: 5080 1.44 - 1.57: 10556 1.57 - 1.69: 0 1.69 - 1.82: 134 Bond restraints: 19013 Sorted by residual: bond pdb=" N GLY F 286 " pdb=" CA GLY F 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.73e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.69e-02 3.50e+03 1.73e+01 bond pdb=" C SER H 88 " pdb=" O SER H 88 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.26e-02 6.30e+03 1.70e+01 bond pdb=" CA SER H 384 " pdb=" CB SER H 384 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.45e-02 4.76e+03 1.69e+01 bond pdb=" C PRO H 166 " pdb=" O PRO H 166 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.18e-02 7.18e+03 1.67e+01 ... (remaining 19008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 23579 2.95 - 5.90: 2142 5.90 - 8.84: 82 8.84 - 11.79: 3 11.79 - 14.74: 3 Bond angle restraints: 25809 Sorted by residual: angle pdb=" CG ARG A 106 " pdb=" CD ARG A 106 " pdb=" NE ARG A 106 " ideal model delta sigma weight residual 112.00 126.74 -14.74 2.20e+00 2.07e-01 4.49e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.81 106.10 5.71 8.60e-01 1.35e+00 4.40e+01 angle pdb=" OD1 ASN H 294 " pdb=" CG ASN H 294 " pdb=" ND2 ASN H 294 " ideal model delta sigma weight residual 122.60 129.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CG ARG I 106 " pdb=" CD ARG I 106 " pdb=" NE ARG I 106 " ideal model delta sigma weight residual 112.00 126.39 -14.39 2.20e+00 2.07e-01 4.28e+01 angle pdb=" CG ARG C 106 " pdb=" CD ARG C 106 " pdb=" NE ARG C 106 " ideal model delta sigma weight residual 112.00 126.32 -14.32 2.20e+00 2.07e-01 4.24e+01 ... (remaining 25804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 11606 22.49 - 44.98: 525 44.98 - 67.46: 97 67.46 - 89.95: 132 89.95 - 112.44: 90 Dihedral angle restraints: 12450 sinusoidal: 6015 harmonic: 6435 Sorted by residual: dihedral pdb=" CA ALA C 9 " pdb=" C ALA C 9 " pdb=" N GLU C 10 " pdb=" CA GLU C 10 " ideal model delta harmonic sigma weight residual 180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY B 57 " pdb=" C GLY B 57 " pdb=" N VAL B 58 " pdb=" CA VAL B 58 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" N CYS A 96 " pdb=" CA CYS A 96 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 12447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1659 0.069 - 0.138: 1029 0.138 - 0.208: 328 0.208 - 0.277: 62 0.277 - 0.346: 7 Chirality restraints: 3085 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.82e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.84e+01 chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.54e+01 ... (remaining 3082 not shown) Planarity restraints: 3215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.079 2.00e-02 2.50e+03 4.26e-02 3.62e+01 pdb=" CG TYR E 281 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 281 " -0.080 2.00e-02 2.50e+03 4.16e-02 3.46e+01 pdb=" CG TYR F 281 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR F 281 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR F 281 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR F 281 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 281 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 281 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 281 " -0.076 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR H 281 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR H 281 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR H 281 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR H 281 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 281 " -0.056 2.00e-02 2.50e+03 ... (remaining 3212 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2089 2.76 - 3.29: 18605 3.29 - 3.83: 34654 3.83 - 4.36: 45039 4.36 - 4.90: 71580 Nonbonded interactions: 171967 Sorted by model distance: nonbonded pdb=" O ASP H 293 " pdb="CA CA H2000 " model vdw 2.222 2.510 nonbonded pdb=" OD2 ASP F 324 " pdb="CA CA F2000 " model vdw 2.233 2.510 nonbonded pdb=" O ASP G 293 " pdb="CA CA G2000 " model vdw 2.251 2.510 nonbonded pdb=" O GLY H 345 " pdb="CA CA H2000 " model vdw 2.257 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.257 2.510 ... (remaining 171962 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 '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and (resid 82 through 469 or resid 501)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.580 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: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 47.120 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 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 : 0.014 0.126 19146 Z= 0.965 Angle : 1.756 14.760 26166 Z= 1.090 Chirality : 0.092 0.346 3085 Planarity : 0.011 0.079 3191 Dihedral : 18.860 112.437 8226 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.16 % Favored : 96.44 % Rotamer: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2246 helix: -1.22 (0.94), residues: 24 sheet: -0.26 (0.16), residues: 885 loop : -0.83 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.014 TRP H 178 HIS 0.019 0.006 HIS H 336 PHE 0.049 0.012 PHE E 446 TYR 0.080 0.015 TYR F 281 ARG 0.036 0.003 ARG H 430 Details of bonding type rmsd link_NAG-ASN : bond 0.02081 ( 24) link_NAG-ASN : angle 5.03337 ( 72) link_ALPHA1-6 : bond 0.00621 ( 8) link_ALPHA1-6 : angle 2.39425 ( 24) link_BETA1-4 : bond 0.01607 ( 47) link_BETA1-4 : angle 4.43032 ( 141) link_ALPHA1-2 : bond 0.01068 ( 4) link_ALPHA1-2 : angle 4.53907 ( 12) link_ALPHA1-3 : bond 0.01404 ( 8) link_ALPHA1-3 : angle 3.01526 ( 24) hydrogen bonds : bond 0.15963 ( 592) hydrogen bonds : angle 8.99901 ( 1581) SS BOND : bond 0.04590 ( 42) SS BOND : angle 2.40278 ( 84) covalent geometry : bond 0.01418 (19013) covalent geometry : angle 1.70521 (25809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 178 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.9173 (p-90) REVERT: H 150 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8210 (tpt90) REVERT: F 178 TRP cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (p-90) REVERT: B 17 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8525 (mm-30) REVERT: C 10 GLU cc_start: 0.8802 (tp30) cc_final: 0.8220 (tp30) REVERT: C 43 GLN cc_start: 0.8894 (mt0) cc_final: 0.8569 (mm-40) REVERT: D 59 PRO cc_start: 0.9517 (Cg_exo) cc_final: 0.9139 (Cg_endo) REVERT: L 2 ILE cc_start: 0.8154 (mt) cc_final: 0.7948 (mt) REVERT: L 17 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8750 (mp0) REVERT: L 54 ARG cc_start: 0.9238 (mtm-85) cc_final: 0.8954 (mtm-85) REVERT: L 81 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8738 (mt-10) REVERT: L 98 THR cc_start: 0.9194 (m) cc_final: 0.8726 (p) REVERT: A 23 LYS cc_start: 0.8942 (tttt) cc_final: 0.8668 (tttp) REVERT: A 81 MET cc_start: 0.9229 (ttp) cc_final: 0.9028 (ttp) outliers start: 4 outliers final: 0 residues processed: 273 average time/residue: 1.4827 time to fit residues: 447.9615 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain F residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 HIS E 465 ASN G 147 ASN H 147 ASN B 6 GLN C 32 ASN D 27 GLN A 31 ASN A 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057005 restraints weight = 31508.317| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.48 r_work: 0.2598 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19146 Z= 0.192 Angle : 0.769 7.600 26166 Z= 0.383 Chirality : 0.049 0.163 3085 Planarity : 0.004 0.040 3191 Dihedral : 14.780 81.566 4293 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 7.11 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2246 helix: -1.16 (0.59), residues: 24 sheet: -0.12 (0.17), residues: 829 loop : -0.19 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 178 HIS 0.004 0.001 HIS F 144 PHE 0.018 0.002 PHE G 410 TYR 0.019 0.002 TYR L 91 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 24) link_NAG-ASN : angle 2.72376 ( 72) link_ALPHA1-6 : bond 0.00474 ( 8) link_ALPHA1-6 : angle 1.26062 ( 24) link_BETA1-4 : bond 0.00417 ( 47) link_BETA1-4 : angle 2.81947 ( 141) link_ALPHA1-2 : bond 0.00482 ( 4) link_ALPHA1-2 : angle 1.75733 ( 12) link_ALPHA1-3 : bond 0.01014 ( 8) link_ALPHA1-3 : angle 2.09819 ( 24) hydrogen bonds : bond 0.05039 ( 592) hydrogen bonds : angle 7.51411 ( 1581) SS BOND : bond 0.00498 ( 42) SS BOND : angle 0.75389 ( 84) covalent geometry : bond 0.00393 (19013) covalent geometry : angle 0.72617 (25809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7852 (mtp-110) REVERT: H 151 ASP cc_start: 0.8765 (p0) cc_final: 0.8528 (p0) REVERT: H 331 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8806 (p) REVERT: B 17 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 24 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: B 39 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8210 (mmmm) REVERT: B 59 PRO cc_start: 0.9090 (Cg_exo) cc_final: 0.8742 (Cg_endo) REVERT: B 81 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8631 (tm-30) REVERT: B 82 ASP cc_start: 0.9195 (m-30) cc_final: 0.8831 (m-30) REVERT: C 43 GLN cc_start: 0.8590 (mt0) cc_final: 0.8275 (mm-40) REVERT: D 59 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: I 3 GLN cc_start: 0.8477 (tt0) cc_final: 0.8207 (tp-100) REVERT: I 23 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8320 (mtpm) REVERT: I 43 GLN cc_start: 0.7626 (mt0) cc_final: 0.6908 (mp10) REVERT: L 2 ILE cc_start: 0.7397 (mt) cc_final: 0.7130 (mt) REVERT: L 17 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8285 (mp0) REVERT: L 54 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8393 (mtm-85) REVERT: L 81 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8581 (mt-10) REVERT: L 98 THR cc_start: 0.8792 (m) cc_final: 0.8203 (p) REVERT: A 23 LYS cc_start: 0.8441 (tttt) cc_final: 0.8186 (ttmt) outliers start: 21 outliers final: 4 residues processed: 251 average time/residue: 1.5336 time to fit residues: 426.6151 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 117 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN F 141 ASN B 6 GLN D 27 GLN I 31 ASN A 62 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.057861 restraints weight = 31424.841| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.45 r_work: 0.2630 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19146 Z= 0.178 Angle : 0.701 6.390 26166 Z= 0.343 Chirality : 0.049 0.178 3085 Planarity : 0.004 0.049 3191 Dihedral : 10.072 63.341 4289 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 8.51 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2246 helix: -1.02 (0.82), residues: 28 sheet: -0.16 (0.18), residues: 819 loop : 0.02 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 178 HIS 0.012 0.001 HIS H 336 PHE 0.018 0.002 PHE G 410 TYR 0.019 0.002 TYR E 121 ARG 0.008 0.001 ARG D 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 24) link_NAG-ASN : angle 2.35391 ( 72) link_ALPHA1-6 : bond 0.00475 ( 8) link_ALPHA1-6 : angle 1.51748 ( 24) link_BETA1-4 : bond 0.00520 ( 47) link_BETA1-4 : angle 2.63669 ( 141) link_ALPHA1-2 : bond 0.00366 ( 4) link_ALPHA1-2 : angle 2.00868 ( 12) link_ALPHA1-3 : bond 0.00757 ( 8) link_ALPHA1-3 : angle 1.82967 ( 24) hydrogen bonds : bond 0.04496 ( 592) hydrogen bonds : angle 6.92775 ( 1581) SS BOND : bond 0.00807 ( 42) SS BOND : angle 0.81432 ( 84) covalent geometry : bond 0.00373 (19013) covalent geometry : angle 0.65961 (25809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9166 (tttt) cc_final: 0.8856 (ttpt) REVERT: H 150 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7857 (mtp-110) REVERT: B 17 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 24 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7964 (ttm-80) REVERT: B 59 PRO cc_start: 0.9132 (Cg_exo) cc_final: 0.8837 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 78 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tt) REVERT: B 81 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8505 (tm-30) REVERT: B 82 ASP cc_start: 0.9287 (m-30) cc_final: 0.8916 (m-30) REVERT: B 104 LYS cc_start: 0.9026 (tppt) cc_final: 0.8800 (tppp) REVERT: B 107 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9077 (mt) REVERT: C 43 GLN cc_start: 0.8546 (mt0) cc_final: 0.8217 (mm-40) REVERT: C 87 ARG cc_start: 0.8303 (mpp80) cc_final: 0.7732 (mpp80) REVERT: C 89 GLU cc_start: 0.8945 (pm20) cc_final: 0.8651 (pm20) REVERT: D 59 PRO cc_start: 0.9178 (Cg_exo) cc_final: 0.8789 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7730 (ptm160) cc_final: 0.6516 (pmt170) REVERT: I 3 GLN cc_start: 0.8418 (tt0) cc_final: 0.8213 (tp-100) REVERT: I 43 GLN cc_start: 0.7723 (mt0) cc_final: 0.7038 (mp10) REVERT: L 54 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8351 (mtm-85) REVERT: L 81 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8524 (mp0) REVERT: L 82 ASP cc_start: 0.8960 (m-30) cc_final: 0.8715 (m-30) REVERT: L 92 ASN cc_start: 0.8812 (t0) cc_final: 0.8564 (t0) REVERT: L 98 THR cc_start: 0.8916 (m) cc_final: 0.8527 (p) REVERT: L 108 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8555 (ttpp) REVERT: A 23 LYS cc_start: 0.8490 (tttt) cc_final: 0.8239 (ttmt) REVERT: A 43 GLN cc_start: 0.8096 (mp10) cc_final: 0.7265 (mp10) outliers start: 18 outliers final: 6 residues processed: 253 average time/residue: 1.5622 time to fit residues: 436.6479 Evaluate side-chains 239 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 114 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN F 141 ASN F 147 ASN B 27 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059362 restraints weight = 31611.957| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.42 r_work: 0.2661 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19146 Z= 0.145 Angle : 0.633 6.088 26166 Z= 0.314 Chirality : 0.046 0.200 3085 Planarity : 0.004 0.041 3191 Dihedral : 7.701 55.405 4289 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 1.19 % Allowed : 9.74 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2246 helix: -0.86 (0.83), residues: 28 sheet: -0.22 (0.18), residues: 843 loop : 0.16 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS H 274 PHE 0.015 0.002 PHE H 410 TYR 0.021 0.002 TYR L 91 ARG 0.007 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 24) link_NAG-ASN : angle 2.18469 ( 72) link_ALPHA1-6 : bond 0.00555 ( 8) link_ALPHA1-6 : angle 1.45978 ( 24) link_BETA1-4 : bond 0.00424 ( 47) link_BETA1-4 : angle 2.25897 ( 141) link_ALPHA1-2 : bond 0.00430 ( 4) link_ALPHA1-2 : angle 1.93999 ( 12) link_ALPHA1-3 : bond 0.00856 ( 8) link_ALPHA1-3 : angle 1.76130 ( 24) hydrogen bonds : bond 0.03960 ( 592) hydrogen bonds : angle 6.64581 ( 1581) SS BOND : bond 0.00276 ( 42) SS BOND : angle 0.68561 ( 84) covalent geometry : bond 0.00311 (19013) covalent geometry : angle 0.59724 (25809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9182 (tttt) cc_final: 0.8861 (ttpt) REVERT: G 93 ASP cc_start: 0.8719 (m-30) cc_final: 0.8351 (t70) REVERT: H 150 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7751 (ttm110) REVERT: H 331 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8854 (p) REVERT: B 17 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 24 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: B 59 PRO cc_start: 0.9237 (Cg_exo) cc_final: 0.8993 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 81 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8472 (tm-30) REVERT: B 82 ASP cc_start: 0.9253 (m-30) cc_final: 0.8929 (m-30) REVERT: B 104 LYS cc_start: 0.8982 (tppt) cc_final: 0.8764 (tppp) REVERT: C 12 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8408 (mtpt) REVERT: C 43 GLN cc_start: 0.8650 (mt0) cc_final: 0.8311 (mm-40) REVERT: C 89 GLU cc_start: 0.8898 (pm20) cc_final: 0.8588 (pm20) REVERT: D 59 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8774 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7684 (ptm160) cc_final: 0.6486 (pmt170) REVERT: I 13 ARG cc_start: 0.8573 (mmt90) cc_final: 0.8335 (mmt90) REVERT: I 43 GLN cc_start: 0.7745 (mt0) cc_final: 0.7157 (mp10) REVERT: L 17 GLU cc_start: 0.7233 (mp0) cc_final: 0.6979 (mp0) REVERT: L 18 ARG cc_start: 0.8786 (ttt90) cc_final: 0.8539 (ttt90) REVERT: L 54 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: L 81 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8543 (mp0) REVERT: L 82 ASP cc_start: 0.8856 (m-30) cc_final: 0.8612 (m-30) REVERT: L 92 ASN cc_start: 0.8828 (t0) cc_final: 0.8600 (t0) REVERT: L 98 THR cc_start: 0.8920 (m) cc_final: 0.8588 (p) REVERT: A 23 LYS cc_start: 0.8524 (tttt) cc_final: 0.8260 (ttmt) REVERT: A 43 GLN cc_start: 0.8115 (mp10) cc_final: 0.7320 (mp10) REVERT: A 73 ASP cc_start: 0.8179 (m-30) cc_final: 0.7620 (t0) outliers start: 23 outliers final: 4 residues processed: 248 average time/residue: 1.4476 time to fit residues: 398.0493 Evaluate side-chains 231 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain I residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 198 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN G 347 HIS F 141 ASN B 93 ASN C 117 ASN I 3 GLN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057386 restraints weight = 31799.515| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.44 r_work: 0.2619 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19146 Z= 0.204 Angle : 0.641 6.046 26166 Z= 0.321 Chirality : 0.046 0.211 3085 Planarity : 0.004 0.041 3191 Dihedral : 7.427 57.067 4289 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.85 % Favored : 96.97 % Rotamer: Outliers : 1.19 % Allowed : 10.52 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2246 helix: -0.74 (0.86), residues: 28 sheet: -0.21 (0.18), residues: 847 loop : 0.12 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.004 0.001 HIS H 336 PHE 0.017 0.002 PHE G 410 TYR 0.023 0.002 TYR L 91 ARG 0.006 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 24) link_NAG-ASN : angle 2.41373 ( 72) link_ALPHA1-6 : bond 0.00360 ( 8) link_ALPHA1-6 : angle 1.59912 ( 24) link_BETA1-4 : bond 0.00403 ( 47) link_BETA1-4 : angle 1.98850 ( 141) link_ALPHA1-2 : bond 0.00228 ( 4) link_ALPHA1-2 : angle 2.03615 ( 12) link_ALPHA1-3 : bond 0.00589 ( 8) link_ALPHA1-3 : angle 2.01096 ( 24) hydrogen bonds : bond 0.04274 ( 592) hydrogen bonds : angle 6.66959 ( 1581) SS BOND : bond 0.00348 ( 42) SS BOND : angle 0.74974 ( 84) covalent geometry : bond 0.00448 (19013) covalent geometry : angle 0.60762 (25809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9216 (tttt) cc_final: 0.8893 (ttpt) REVERT: G 93 ASP cc_start: 0.8730 (m-30) cc_final: 0.8393 (t70) REVERT: H 150 ARG cc_start: 0.8046 (ttt180) cc_final: 0.7777 (ttm110) REVERT: H 331 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8919 (p) REVERT: B 17 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8293 (mm-30) REVERT: B 24 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7957 (ttm-80) REVERT: B 59 PRO cc_start: 0.9199 (Cg_exo) cc_final: 0.8874 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 81 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8467 (tm-30) REVERT: B 82 ASP cc_start: 0.9203 (m-30) cc_final: 0.8851 (m-30) REVERT: B 104 LYS cc_start: 0.8976 (tppt) cc_final: 0.8742 (tppp) REVERT: C 43 GLN cc_start: 0.8639 (mt0) cc_final: 0.8258 (mm-40) REVERT: D 17 GLU cc_start: 0.7791 (mp0) cc_final: 0.7454 (mp0) REVERT: D 61 ARG cc_start: 0.8939 (ptp90) cc_final: 0.8569 (ptp90) REVERT: I 43 GLN cc_start: 0.7755 (mt0) cc_final: 0.7209 (mp10) REVERT: I 52 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (mm) REVERT: I 73 ASP cc_start: 0.8202 (m-30) cc_final: 0.7982 (t0) REVERT: L 17 GLU cc_start: 0.7260 (mp0) cc_final: 0.6884 (mp0) REVERT: L 54 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8397 (mtm-85) REVERT: L 81 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8532 (mp0) REVERT: L 82 ASP cc_start: 0.8828 (m-30) cc_final: 0.8602 (m-30) REVERT: L 92 ASN cc_start: 0.8828 (t0) cc_final: 0.8512 (m-40) REVERT: L 98 THR cc_start: 0.9006 (m) cc_final: 0.8674 (p) REVERT: A 13 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8090 (mtp85) REVERT: A 23 LYS cc_start: 0.8482 (tttt) cc_final: 0.8225 (ttmt) REVERT: A 43 GLN cc_start: 0.8109 (mp10) cc_final: 0.7284 (mp10) REVERT: A 73 ASP cc_start: 0.8304 (m-30) cc_final: 0.7713 (t0) outliers start: 23 outliers final: 4 residues processed: 230 average time/residue: 1.4624 time to fit residues: 372.3987 Evaluate side-chains 225 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN B 93 ASN C 117 ASN I 3 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.056899 restraints weight = 31882.771| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.45 r_work: 0.2608 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19146 Z= 0.224 Angle : 0.640 6.325 26166 Z= 0.322 Chirality : 0.046 0.207 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.392 58.075 4289 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 1.24 % Allowed : 10.98 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2246 helix: -0.75 (0.82), residues: 28 sheet: -0.25 (0.17), residues: 847 loop : 0.12 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 144 PHE 0.017 0.002 PHE G 410 TYR 0.022 0.002 TYR L 91 ARG 0.008 0.001 ARG I 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 24) link_NAG-ASN : angle 2.43040 ( 72) link_ALPHA1-6 : bond 0.00315 ( 8) link_ALPHA1-6 : angle 1.59471 ( 24) link_BETA1-4 : bond 0.00389 ( 47) link_BETA1-4 : angle 1.81823 ( 141) link_ALPHA1-2 : bond 0.00193 ( 4) link_ALPHA1-2 : angle 2.05117 ( 12) link_ALPHA1-3 : bond 0.00564 ( 8) link_ALPHA1-3 : angle 2.01364 ( 24) hydrogen bonds : bond 0.04287 ( 592) hydrogen bonds : angle 6.65630 ( 1581) SS BOND : bond 0.00367 ( 42) SS BOND : angle 0.70217 ( 84) covalent geometry : bond 0.00494 (19013) covalent geometry : angle 0.60924 (25809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9231 (tttt) cc_final: 0.8899 (ttpt) REVERT: G 93 ASP cc_start: 0.8706 (m-30) cc_final: 0.8391 (t70) REVERT: H 150 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7774 (ttm110) REVERT: H 331 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8959 (p) REVERT: B 17 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 24 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7919 (ttm-80) REVERT: B 59 PRO cc_start: 0.9154 (Cg_exo) cc_final: 0.8852 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 81 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8437 (tm-30) REVERT: B 82 ASP cc_start: 0.9196 (m-30) cc_final: 0.8844 (m-30) REVERT: B 104 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8758 (tppp) REVERT: B 107 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9014 (mt) REVERT: C 12 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8529 (mtpt) REVERT: C 43 GLN cc_start: 0.8607 (mt0) cc_final: 0.8238 (mm-40) REVERT: D 4 MET cc_start: 0.8692 (mmm) cc_final: 0.8397 (mmm) REVERT: D 17 GLU cc_start: 0.7741 (mp0) cc_final: 0.7438 (mp0) REVERT: D 104 LYS cc_start: 0.8818 (tptm) cc_final: 0.8531 (tptp) REVERT: I 23 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8206 (mtpm) REVERT: I 38 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7373 (ptt180) REVERT: I 43 GLN cc_start: 0.7744 (mt0) cc_final: 0.7234 (mp10) REVERT: I 52 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8395 (mm) REVERT: I 73 ASP cc_start: 0.8263 (m-30) cc_final: 0.8036 (t0) REVERT: I 117 ASN cc_start: 0.8429 (m110) cc_final: 0.8066 (m110) REVERT: L 17 GLU cc_start: 0.7284 (mp0) cc_final: 0.6847 (mp0) REVERT: L 45 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8136 (ttt-90) REVERT: L 54 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8438 (mtm-85) REVERT: L 61 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.8359 (ptp-170) REVERT: L 81 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8542 (mp0) REVERT: L 82 ASP cc_start: 0.8807 (m-30) cc_final: 0.8454 (m-30) REVERT: L 98 THR cc_start: 0.9035 (m) cc_final: 0.8691 (p) REVERT: A 23 LYS cc_start: 0.8455 (tttt) cc_final: 0.8201 (ttmt) REVERT: A 43 GLN cc_start: 0.8163 (mp10) cc_final: 0.7354 (mp10) outliers start: 24 outliers final: 6 residues processed: 236 average time/residue: 1.5054 time to fit residues: 393.5521 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 207 optimal weight: 0.0060 chunk 158 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN C 117 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.056749 restraints weight = 31644.136| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.43 r_work: 0.2606 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19146 Z= 0.224 Angle : 0.641 6.531 26166 Z= 0.323 Chirality : 0.046 0.209 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.376 58.543 4289 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 1.03 % Allowed : 11.49 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2246 helix: -0.72 (0.83), residues: 28 sheet: -0.26 (0.17), residues: 847 loop : 0.13 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS H 336 PHE 0.017 0.002 PHE G 410 TYR 0.021 0.002 TYR L 91 ARG 0.007 0.001 ARG I 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 24) link_NAG-ASN : angle 2.42918 ( 72) link_ALPHA1-6 : bond 0.00304 ( 8) link_ALPHA1-6 : angle 1.61045 ( 24) link_BETA1-4 : bond 0.00384 ( 47) link_BETA1-4 : angle 1.71730 ( 141) link_ALPHA1-2 : bond 0.00180 ( 4) link_ALPHA1-2 : angle 2.06156 ( 12) link_ALPHA1-3 : bond 0.00552 ( 8) link_ALPHA1-3 : angle 2.02357 ( 24) hydrogen bonds : bond 0.04284 ( 592) hydrogen bonds : angle 6.66819 ( 1581) SS BOND : bond 0.00366 ( 42) SS BOND : angle 0.80820 ( 84) covalent geometry : bond 0.00494 (19013) covalent geometry : angle 0.61101 (25809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9240 (tttt) cc_final: 0.8906 (ttpt) REVERT: G 93 ASP cc_start: 0.8709 (m-30) cc_final: 0.8407 (t70) REVERT: H 150 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7780 (ttm110) REVERT: H 331 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8965 (p) REVERT: B 17 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 24 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7881 (ttm-80) REVERT: B 59 PRO cc_start: 0.9142 (Cg_exo) cc_final: 0.8824 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 81 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8388 (tm-30) REVERT: B 82 ASP cc_start: 0.9211 (m-30) cc_final: 0.8891 (m-30) REVERT: B 104 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8769 (tppp) REVERT: B 107 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.9025 (mt) REVERT: C 23 LYS cc_start: 0.8498 (mtpm) cc_final: 0.8242 (mmmt) REVERT: C 43 GLN cc_start: 0.8534 (mt0) cc_final: 0.8185 (mm-40) REVERT: D 17 GLU cc_start: 0.7750 (mp0) cc_final: 0.7429 (mp0) REVERT: D 33 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8396 (tm) REVERT: D 61 ARG cc_start: 0.8946 (ptp90) cc_final: 0.8650 (ptp90) REVERT: D 104 LYS cc_start: 0.8829 (tptm) cc_final: 0.8532 (tptp) REVERT: I 23 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8209 (mtpm) REVERT: I 38 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7395 (ptt180) REVERT: I 43 GLN cc_start: 0.7730 (mt0) cc_final: 0.7239 (mp10) REVERT: I 52 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8430 (mm) REVERT: I 73 ASP cc_start: 0.8303 (m-30) cc_final: 0.8046 (t0) REVERT: I 117 ASN cc_start: 0.8447 (m110) cc_final: 0.8082 (m-40) REVERT: L 17 GLU cc_start: 0.7326 (mp0) cc_final: 0.6879 (mp0) REVERT: L 45 ARG cc_start: 0.8388 (ttt-90) cc_final: 0.8152 (ttt-90) REVERT: L 54 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8396 (mtm-85) REVERT: L 61 ARG cc_start: 0.8743 (ptt-90) cc_final: 0.8392 (ptp-170) REVERT: L 81 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8531 (mp0) REVERT: L 82 ASP cc_start: 0.8809 (m-30) cc_final: 0.8464 (m-30) REVERT: L 92 ASN cc_start: 0.8822 (t0) cc_final: 0.8601 (m-40) REVERT: L 98 THR cc_start: 0.9044 (m) cc_final: 0.8682 (p) REVERT: A 23 LYS cc_start: 0.8450 (tttt) cc_final: 0.8186 (ttmt) REVERT: A 43 GLN cc_start: 0.8101 (mp10) cc_final: 0.7541 (mp10) REVERT: A 63 LYS cc_start: 0.9379 (mtpp) cc_final: 0.9118 (ptpp) outliers start: 20 outliers final: 6 residues processed: 237 average time/residue: 1.5457 time to fit residues: 404.7723 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 120 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN C 117 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.056486 restraints weight = 31801.428| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.44 r_work: 0.2599 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19146 Z= 0.238 Angle : 0.647 7.116 26166 Z= 0.326 Chirality : 0.046 0.210 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.395 59.283 4289 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 11.96 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2246 helix: -0.74 (0.82), residues: 28 sheet: -0.26 (0.17), residues: 847 loop : 0.13 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS H 336 PHE 0.017 0.002 PHE G 410 TYR 0.020 0.002 TYR L 91 ARG 0.007 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 24) link_NAG-ASN : angle 2.45707 ( 72) link_ALPHA1-6 : bond 0.00276 ( 8) link_ALPHA1-6 : angle 1.62358 ( 24) link_BETA1-4 : bond 0.00378 ( 47) link_BETA1-4 : angle 1.68052 ( 141) link_ALPHA1-2 : bond 0.00156 ( 4) link_ALPHA1-2 : angle 2.08000 ( 12) link_ALPHA1-3 : bond 0.00522 ( 8) link_ALPHA1-3 : angle 2.05983 ( 24) hydrogen bonds : bond 0.04325 ( 592) hydrogen bonds : angle 6.67975 ( 1581) SS BOND : bond 0.00385 ( 42) SS BOND : angle 0.80188 ( 84) covalent geometry : bond 0.00525 (19013) covalent geometry : angle 0.61818 (25809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9246 (tttt) cc_final: 0.8908 (ttpt) REVERT: G 93 ASP cc_start: 0.8700 (m-30) cc_final: 0.8428 (t70) REVERT: H 150 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7759 (ttm110) REVERT: H 331 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 17 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 24 ARG cc_start: 0.8415 (ttp80) cc_final: 0.7910 (ttm-80) REVERT: B 59 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8788 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 81 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8392 (tm-30) REVERT: B 82 ASP cc_start: 0.9221 (m-30) cc_final: 0.8878 (m-30) REVERT: B 104 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8759 (tppp) REVERT: C 10 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: C 23 LYS cc_start: 0.8507 (mtpm) cc_final: 0.8269 (mmmt) REVERT: C 43 GLN cc_start: 0.8548 (mt0) cc_final: 0.8186 (mm-40) REVERT: D 17 GLU cc_start: 0.7749 (mp0) cc_final: 0.7379 (mp0) REVERT: D 33 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8405 (tm) REVERT: D 61 ARG cc_start: 0.8930 (ptp90) cc_final: 0.8677 (ptp90) REVERT: I 23 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8189 (mtpm) REVERT: I 38 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7380 (ptt180) REVERT: I 43 GLN cc_start: 0.7735 (mt0) cc_final: 0.7242 (mp10) REVERT: I 52 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8428 (mm) REVERT: I 73 ASP cc_start: 0.8299 (m-30) cc_final: 0.8033 (t0) REVERT: I 117 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m-40) REVERT: L 17 GLU cc_start: 0.7334 (mp0) cc_final: 0.6971 (mp0) REVERT: L 45 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8046 (ttt180) REVERT: L 54 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: L 61 ARG cc_start: 0.8750 (ptt-90) cc_final: 0.8370 (ptp-170) REVERT: L 81 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8534 (mp0) REVERT: L 82 ASP cc_start: 0.8821 (m-30) cc_final: 0.8519 (m-30) REVERT: L 98 THR cc_start: 0.9042 (m) cc_final: 0.8683 (p) REVERT: A 23 LYS cc_start: 0.8439 (tttt) cc_final: 0.8183 (ttmt) REVERT: A 43 GLN cc_start: 0.8101 (mp10) cc_final: 0.7523 (mp10) REVERT: A 63 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9122 (ptpp) REVERT: A 73 ASP cc_start: 0.8404 (m-30) cc_final: 0.7225 (p0) outliers start: 19 outliers final: 6 residues processed: 232 average time/residue: 1.5539 time to fit residues: 399.0037 Evaluate side-chains 231 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 402 ASN H 465 ASN B 27 GLN B 93 ASN C 117 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.055711 restraints weight = 31956.935| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.44 r_work: 0.2584 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19146 Z= 0.274 Angle : 0.668 7.653 26166 Z= 0.337 Chirality : 0.047 0.209 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.574 62.224 4289 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 1.08 % Allowed : 11.96 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2246 helix: -0.73 (0.83), residues: 28 sheet: -0.29 (0.17), residues: 847 loop : 0.10 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 178 HIS 0.004 0.001 HIS H 336 PHE 0.018 0.002 PHE G 410 TYR 0.021 0.002 TYR L 91 ARG 0.007 0.001 ARG I 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 24) link_NAG-ASN : angle 2.57588 ( 72) link_ALPHA1-6 : bond 0.00194 ( 8) link_ALPHA1-6 : angle 1.67580 ( 24) link_BETA1-4 : bond 0.00377 ( 47) link_BETA1-4 : angle 1.66734 ( 141) link_ALPHA1-2 : bond 0.00141 ( 4) link_ALPHA1-2 : angle 2.13900 ( 12) link_ALPHA1-3 : bond 0.00425 ( 8) link_ALPHA1-3 : angle 2.17896 ( 24) hydrogen bonds : bond 0.04523 ( 592) hydrogen bonds : angle 6.75565 ( 1581) SS BOND : bond 0.00424 ( 42) SS BOND : angle 0.82825 ( 84) covalent geometry : bond 0.00608 (19013) covalent geometry : angle 0.63874 (25809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9235 (tttt) cc_final: 0.8897 (ttpt) REVERT: G 93 ASP cc_start: 0.8718 (m-30) cc_final: 0.8410 (t70) REVERT: H 150 ARG cc_start: 0.8009 (ttt180) cc_final: 0.7769 (ttm110) REVERT: H 331 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8996 (p) REVERT: B 17 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8286 (mm-30) REVERT: B 24 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7843 (ttm-80) REVERT: B 59 PRO cc_start: 0.9099 (Cg_exo) cc_final: 0.8725 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 81 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8393 (tm-30) REVERT: B 82 ASP cc_start: 0.9219 (m-30) cc_final: 0.8855 (m-30) REVERT: B 104 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8761 (tppp) REVERT: C 10 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: C 23 LYS cc_start: 0.8513 (mtpm) cc_final: 0.8280 (mmmt) REVERT: C 43 GLN cc_start: 0.8573 (mt0) cc_final: 0.8199 (mm-40) REVERT: D 17 GLU cc_start: 0.7762 (mp0) cc_final: 0.7387 (mp0) REVERT: D 61 ARG cc_start: 0.8938 (ptp90) cc_final: 0.8653 (ptp90) REVERT: I 23 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8173 (mtpm) REVERT: I 38 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7372 (ptt180) REVERT: I 43 GLN cc_start: 0.7764 (mt0) cc_final: 0.7260 (mp10) REVERT: I 52 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (mm) REVERT: I 73 ASP cc_start: 0.8307 (m-30) cc_final: 0.8044 (t0) REVERT: L 17 GLU cc_start: 0.7355 (mp0) cc_final: 0.6976 (mp0) REVERT: L 45 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.8063 (ttt180) REVERT: L 54 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8488 (mtm-85) REVERT: L 61 ARG cc_start: 0.8769 (ptt-90) cc_final: 0.8367 (ptp-170) REVERT: L 81 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8533 (mp0) REVERT: L 82 ASP cc_start: 0.8836 (m-30) cc_final: 0.8534 (m-30) REVERT: L 98 THR cc_start: 0.9045 (m) cc_final: 0.8683 (p) REVERT: A 23 LYS cc_start: 0.8428 (tttt) cc_final: 0.8164 (ttmt) REVERT: A 43 GLN cc_start: 0.8102 (mp10) cc_final: 0.7517 (mp10) REVERT: A 63 LYS cc_start: 0.9384 (mtpp) cc_final: 0.9116 (ptpp) REVERT: A 73 ASP cc_start: 0.8422 (m-30) cc_final: 0.7351 (p0) outliers start: 21 outliers final: 7 residues processed: 238 average time/residue: 1.5732 time to fit residues: 416.1307 Evaluate side-chains 237 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 120 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN C 117 ASN A 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.056531 restraints weight = 31784.426| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.43 r_work: 0.2594 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19146 Z= 0.193 Angle : 0.804 59.197 26166 Z= 0.432 Chirality : 0.045 0.201 3085 Planarity : 0.004 0.041 3191 Dihedral : 7.530 61.471 4289 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 0.88 % Allowed : 12.27 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2246 helix: -0.75 (0.82), residues: 28 sheet: -0.32 (0.17), residues: 847 loop : 0.11 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 178 HIS 0.004 0.001 HIS H 336 PHE 0.017 0.002 PHE F 410 TYR 0.021 0.002 TYR L 91 ARG 0.007 0.001 ARG I 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 24) link_NAG-ASN : angle 2.58022 ( 72) link_ALPHA1-6 : bond 0.00313 ( 8) link_ALPHA1-6 : angle 1.67002 ( 24) link_BETA1-4 : bond 0.00354 ( 47) link_BETA1-4 : angle 1.65443 ( 141) link_ALPHA1-2 : bond 0.00164 ( 4) link_ALPHA1-2 : angle 2.11318 ( 12) link_ALPHA1-3 : bond 0.00490 ( 8) link_ALPHA1-3 : angle 2.16436 ( 24) hydrogen bonds : bond 0.04374 ( 592) hydrogen bonds : angle 6.76933 ( 1581) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.76244 ( 84) covalent geometry : bond 0.00413 (19013) covalent geometry : angle 0.78147 (25809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9247 (tttt) cc_final: 0.8910 (ttpt) REVERT: G 93 ASP cc_start: 0.8706 (m-30) cc_final: 0.8406 (t70) REVERT: H 150 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7761 (ttm110) REVERT: H 331 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 17 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 24 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7847 (ttm-80) REVERT: B 59 PRO cc_start: 0.9077 (Cg_exo) cc_final: 0.8724 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 81 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8383 (tm-30) REVERT: B 82 ASP cc_start: 0.9212 (m-30) cc_final: 0.8883 (m-30) REVERT: B 104 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8747 (tppp) REVERT: C 23 LYS cc_start: 0.8502 (mtpm) cc_final: 0.8268 (mmmt) REVERT: C 43 GLN cc_start: 0.8567 (mt0) cc_final: 0.8194 (mm-40) REVERT: C 100 ARG cc_start: 0.8646 (tpt-90) cc_final: 0.8162 (tpp80) REVERT: D 17 GLU cc_start: 0.7762 (mp0) cc_final: 0.7388 (mp0) REVERT: D 61 ARG cc_start: 0.8931 (ptp90) cc_final: 0.8652 (ptp90) REVERT: I 23 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8177 (mtpm) REVERT: I 38 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7361 (ptt180) REVERT: I 43 GLN cc_start: 0.7759 (mt0) cc_final: 0.7260 (mp10) REVERT: I 52 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8434 (mm) REVERT: I 73 ASP cc_start: 0.8293 (m-30) cc_final: 0.8021 (t0) REVERT: L 17 GLU cc_start: 0.7348 (mp0) cc_final: 0.6964 (mp0) REVERT: L 45 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.8049 (ttt180) REVERT: L 54 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: L 61 ARG cc_start: 0.8768 (ptt-90) cc_final: 0.8357 (ptp-170) REVERT: L 81 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8531 (mp0) REVERT: L 82 ASP cc_start: 0.8841 (m-30) cc_final: 0.8534 (m-30) REVERT: L 98 THR cc_start: 0.9042 (m) cc_final: 0.8677 (p) REVERT: A 23 LYS cc_start: 0.8421 (tttt) cc_final: 0.8150 (ttmt) REVERT: A 43 GLN cc_start: 0.8091 (mp10) cc_final: 0.7506 (mp10) REVERT: A 63 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9112 (ptpp) REVERT: A 73 ASP cc_start: 0.8416 (m-30) cc_final: 0.7358 (p0) outliers start: 17 outliers final: 6 residues processed: 235 average time/residue: 1.5482 time to fit residues: 401.8330 Evaluate side-chains 236 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 150 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN B 93 ASN C 117 ASN A 117 ASN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.056457 restraints weight = 31827.237| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.44 r_work: 0.2595 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19146 Z= 0.193 Angle : 0.804 59.197 26166 Z= 0.432 Chirality : 0.045 0.201 3085 Planarity : 0.004 0.041 3191 Dihedral : 7.530 61.471 4289 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 0.62 % Allowed : 12.58 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2246 helix: -0.75 (0.82), residues: 28 sheet: -0.32 (0.17), residues: 847 loop : 0.11 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 178 HIS 0.004 0.001 HIS H 336 PHE 0.017 0.002 PHE F 410 TYR 0.021 0.002 TYR L 91 ARG 0.007 0.001 ARG I 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 24) link_NAG-ASN : angle 2.58022 ( 72) link_ALPHA1-6 : bond 0.00313 ( 8) link_ALPHA1-6 : angle 1.67002 ( 24) link_BETA1-4 : bond 0.00354 ( 47) link_BETA1-4 : angle 1.65443 ( 141) link_ALPHA1-2 : bond 0.00164 ( 4) link_ALPHA1-2 : angle 2.11318 ( 12) link_ALPHA1-3 : bond 0.00490 ( 8) link_ALPHA1-3 : angle 2.16436 ( 24) hydrogen bonds : bond 0.04374 ( 592) hydrogen bonds : angle 6.76933 ( 1581) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.76244 ( 84) covalent geometry : bond 0.00413 (19013) covalent geometry : angle 0.78147 (25809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15704.31 seconds wall clock time: 273 minutes 21.27 seconds (16401.27 seconds total)