Starting phenix.real_space_refine on Sun Aug 24 09:05:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3q_29708/08_2025/8g3q_29708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3q_29708/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g3q_29708/08_2025/8g3q_29708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3q_29708/08_2025/8g3q_29708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3q_29708/08_2025/8g3q_29708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3q_29708/08_2025/8g3q_29708.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.92, per 1000 atoms: 0.26 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: 2.22 Conformation dependent library (CDL) restraints added in 810.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.77 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: 3.98 Time building geometry restraints manager: 2.77 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 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.830 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (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 ARG 0.036 0.003 ARG H 430 TYR 0.080 0.015 TYR F 281 PHE 0.049 0.012 PHE E 446 TRP 0.076 0.014 TRP H 178 HIS 0.019 0.006 HIS H 336 Details of bonding type rmsd covalent geometry : bond 0.01418 (19013) covalent geometry : angle 1.70521 (25809) SS BOND : bond 0.04590 ( 42) SS BOND : angle 2.40278 ( 84) hydrogen bonds : bond 0.15963 ( 592) hydrogen bonds : angle 8.99901 ( 1581) 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) 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_NAG-ASN : bond 0.02081 ( 24) link_NAG-ASN : angle 5.03337 ( 72) *********************** 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 : 0.746 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: 0.8516 (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: 0.8042 time to fit residues: 241.1478 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 : 0.732 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN G 147 ASN H 147 ASN B 6 GLN D 27 GLN A 31 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 = 0.3208 r_free = 0.3208 target = 0.081498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057549 restraints weight = 31473.073| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.47 r_work: 0.2612 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1713 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= 0.180 Angle : 0.762 7.283 26166 Z= 0.374 Chirality : 0.049 0.184 3085 Planarity : 0.004 0.043 3191 Dihedral : 14.275 79.107 4293 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 1.08 % Allowed : 7.22 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2246 helix: -1.21 (0.58), residues: 24 sheet: -0.10 (0.18), residues: 813 loop : -0.22 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.017 0.002 TYR D 91 PHE 0.016 0.002 PHE G 410 TRP 0.022 0.002 TRP G 178 HIS 0.004 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00380 (19013) covalent geometry : angle 0.71933 (25809) SS BOND : bond 0.00371 ( 42) SS BOND : angle 0.70531 ( 84) hydrogen bonds : bond 0.04690 ( 592) hydrogen bonds : angle 7.46249 ( 1581) link_ALPHA1-2 : bond 0.00454 ( 4) link_ALPHA1-2 : angle 1.62429 ( 12) link_ALPHA1-3 : bond 0.00828 ( 8) link_ALPHA1-3 : angle 2.10399 ( 24) link_ALPHA1-6 : bond 0.00536 ( 8) link_ALPHA1-6 : angle 1.22789 ( 24) link_BETA1-4 : bond 0.00375 ( 47) link_BETA1-4 : angle 2.87838 ( 141) link_NAG-ASN : bond 0.00372 ( 24) link_NAG-ASN : angle 2.55854 ( 72) *********************** 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 266 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8086 (ttt180) cc_final: 0.7864 (mtp-110) REVERT: H 151 ASP cc_start: 0.8735 (p0) cc_final: 0.8482 (p0) REVERT: B 17 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 24 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7927 (ttm-80) REVERT: B 59 PRO cc_start: 0.9108 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 81 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8648 (tm-30) REVERT: B 82 ASP cc_start: 0.9207 (m-30) cc_final: 0.8841 (m-30) REVERT: C 43 GLN cc_start: 0.8579 (mt0) cc_final: 0.8278 (mm-40) REVERT: C 98 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7979 (ttt-90) REVERT: D 59 PRO cc_start: 0.9179 (Cg_exo) cc_final: 0.8746 (Cg_endo) REVERT: I 3 GLN cc_start: 0.8475 (tt0) cc_final: 0.8214 (tp-100) REVERT: I 23 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8339 (mtpm) REVERT: I 43 GLN cc_start: 0.7655 (mt0) cc_final: 0.6947 (mp10) REVERT: L 2 ILE cc_start: 0.7514 (mt) cc_final: 0.7240 (mt) REVERT: L 17 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8278 (mp0) REVERT: L 45 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.8080 (ttt-90) REVERT: L 54 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8359 (mtm-85) REVERT: L 81 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8596 (mt-10) REVERT: L 98 THR cc_start: 0.8807 (m) cc_final: 0.8220 (p) REVERT: A 23 LYS cc_start: 0.8462 (tttt) cc_final: 0.8203 (ttmt) outliers start: 21 outliers final: 4 residues processed: 253 average time/residue: 0.8058 time to fit residues: 223.9831 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain C residue 98 ARG 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 150 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 347 HIS H 465 ASN F 141 ASN C 117 ASN D 27 GLN I 31 ASN A 62 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.079906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.056026 restraints weight = 32026.800| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.42 r_work: 0.2581 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19146 Z= 0.239 Angle : 0.733 6.678 26166 Z= 0.359 Chirality : 0.050 0.184 3085 Planarity : 0.004 0.047 3191 Dihedral : 10.328 67.652 4289 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2246 helix: -0.09 (0.90), residues: 24 sheet: -0.19 (0.18), residues: 810 loop : 0.02 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.021 0.002 TYR E 121 PHE 0.019 0.002 PHE G 410 TRP 0.021 0.002 TRP H 178 HIS 0.010 0.001 HIS H 336 Details of bonding type rmsd covalent geometry : bond 0.00522 (19013) covalent geometry : angle 0.68862 (25809) SS BOND : bond 0.00411 ( 42) SS BOND : angle 0.89317 ( 84) hydrogen bonds : bond 0.04868 ( 592) hydrogen bonds : angle 7.06746 ( 1581) link_ALPHA1-2 : bond 0.00206 ( 4) link_ALPHA1-2 : angle 2.11159 ( 12) link_ALPHA1-3 : bond 0.00546 ( 8) link_ALPHA1-3 : angle 2.05108 ( 24) link_ALPHA1-6 : bond 0.00308 ( 8) link_ALPHA1-6 : angle 1.61444 ( 24) link_BETA1-4 : bond 0.00524 ( 47) link_BETA1-4 : angle 2.72221 ( 141) link_NAG-ASN : bond 0.00502 ( 24) link_NAG-ASN : angle 2.60787 ( 72) *********************** 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 251 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9207 (tttt) cc_final: 0.8886 (ttpt) REVERT: G 93 ASP cc_start: 0.8720 (m-30) cc_final: 0.8336 (t70) REVERT: H 150 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7870 (mtp-110) REVERT: H 331 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8891 (p) REVERT: B 17 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 24 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: B 54 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: B 59 PRO cc_start: 0.9107 (Cg_exo) cc_final: 0.8781 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 81 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8504 (tm-30) REVERT: B 82 ASP cc_start: 0.9309 (m-30) cc_final: 0.8932 (m-30) REVERT: C 43 GLN cc_start: 0.8606 (mt0) cc_final: 0.8256 (mm-40) REVERT: C 45 LEU cc_start: 0.9229 (mt) cc_final: 0.9017 (mm) REVERT: C 67 ARG cc_start: 0.8630 (ptt90) cc_final: 0.8348 (ptm-80) REVERT: C 98 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8009 (ttt-90) REVERT: D 59 PRO cc_start: 0.9149 (Cg_exo) cc_final: 0.8702 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7746 (ptm160) cc_final: 0.6533 (pmt170) REVERT: I 3 GLN cc_start: 0.8446 (tt0) cc_final: 0.8236 (tp-100) REVERT: I 13 ARG cc_start: 0.8564 (mmt90) cc_final: 0.8352 (mmt90) REVERT: I 43 GLN cc_start: 0.7705 (mt0) cc_final: 0.7011 (mp10) REVERT: I 117 ASN cc_start: 0.8342 (m110) cc_final: 0.8100 (m110) REVERT: L 54 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: L 81 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8532 (mp0) REVERT: L 82 ASP cc_start: 0.8975 (m-30) cc_final: 0.8723 (m-30) REVERT: L 92 ASN cc_start: 0.8819 (t0) cc_final: 0.8615 (t0) REVERT: L 98 THR cc_start: 0.8936 (m) cc_final: 0.8523 (p) REVERT: L 108 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: A 23 LYS cc_start: 0.8496 (tttt) cc_final: 0.8237 (ttmt) REVERT: A 43 GLN cc_start: 0.8091 (mp10) cc_final: 0.7176 (mp10) outliers start: 19 outliers final: 5 residues processed: 240 average time/residue: 0.7253 time to fit residues: 191.4025 Evaluate side-chains 231 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 C residue 98 ARG 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 203 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 A 117 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056066 restraints weight = 31767.385| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.42 r_work: 0.2587 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19146 Z= 0.240 Angle : 0.683 6.610 26166 Z= 0.340 Chirality : 0.047 0.197 3085 Planarity : 0.004 0.041 3191 Dihedral : 8.419 64.168 4289 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 0.98 % Allowed : 9.79 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2246 helix: -0.82 (0.85), residues: 28 sheet: -0.28 (0.17), residues: 847 loop : 0.01 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.019 0.002 TYR D 91 PHE 0.019 0.002 PHE G 410 TRP 0.018 0.002 TRP H 178 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00529 (19013) covalent geometry : angle 0.64335 (25809) SS BOND : bond 0.00409 ( 42) SS BOND : angle 0.81650 ( 84) hydrogen bonds : bond 0.04535 ( 592) hydrogen bonds : angle 6.89747 ( 1581) link_ALPHA1-2 : bond 0.00187 ( 4) link_ALPHA1-2 : angle 2.11677 ( 12) link_ALPHA1-3 : bond 0.00537 ( 8) link_ALPHA1-3 : angle 2.06341 ( 24) link_ALPHA1-6 : bond 0.00312 ( 8) link_ALPHA1-6 : angle 1.56519 ( 24) link_BETA1-4 : bond 0.00396 ( 47) link_BETA1-4 : angle 2.39929 ( 141) link_NAG-ASN : bond 0.00467 ( 24) link_NAG-ASN : angle 2.50091 ( 72) *********************** 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 244 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 ASP cc_start: 0.8718 (m-30) cc_final: 0.8329 (t70) REVERT: H 150 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7854 (mtp-110) REVERT: H 331 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8931 (p) REVERT: B 17 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8241 (mm-30) REVERT: B 24 ARG cc_start: 0.8382 (ttp80) cc_final: 0.7924 (ttm-80) REVERT: B 59 PRO cc_start: 0.9165 (Cg_exo) cc_final: 0.8796 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 81 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8479 (tm-30) REVERT: B 82 ASP cc_start: 0.9225 (m-30) cc_final: 0.8948 (m-30) REVERT: C 12 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8285 (mtpt) REVERT: C 43 GLN cc_start: 0.8668 (mt0) cc_final: 0.8310 (mm-40) REVERT: C 89 GLU cc_start: 0.8940 (pm20) cc_final: 0.8665 (pm20) REVERT: C 98 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (ttt-90) REVERT: D 59 PRO cc_start: 0.9089 (Cg_exo) cc_final: 0.8684 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7563 (ptm160) cc_final: 0.6506 (pmt170) REVERT: I 13 ARG cc_start: 0.8554 (mmt90) cc_final: 0.8337 (mmt90) REVERT: I 43 GLN cc_start: 0.7758 (mt0) cc_final: 0.7078 (mp10) REVERT: I 52 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (mm) REVERT: I 117 ASN cc_start: 0.8410 (m110) cc_final: 0.8158 (m110) REVERT: L 17 GLU cc_start: 0.7368 (mp0) cc_final: 0.6915 (mp0) REVERT: L 54 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8385 (mtm-85) REVERT: L 81 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8495 (mp0) REVERT: L 82 ASP cc_start: 0.8878 (m-30) cc_final: 0.8624 (m-30) REVERT: L 98 THR cc_start: 0.8940 (m) cc_final: 0.8588 (p) REVERT: A 23 LYS cc_start: 0.8486 (tttt) cc_final: 0.8226 (ttmt) REVERT: A 43 GLN cc_start: 0.8147 (mp10) cc_final: 0.7281 (mp10) REVERT: A 73 ASP cc_start: 0.8241 (m-30) cc_final: 0.7647 (t0) REVERT: A 111 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8546 (mm-30) outliers start: 19 outliers final: 5 residues processed: 233 average time/residue: 0.7178 time to fit residues: 183.6521 Evaluate side-chains 227 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 C residue 98 ARG Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 156 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 F 147 ASN B 93 ASN I 3 GLN A 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057376 restraints weight = 31702.757| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.43 r_work: 0.2619 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2336 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= 0.183 Angle : 0.634 6.205 26166 Z= 0.318 Chirality : 0.046 0.200 3085 Planarity : 0.004 0.041 3191 Dihedral : 7.611 59.054 4289 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 9.85 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2246 helix: -0.78 (0.84), residues: 28 sheet: -0.27 (0.17), residues: 847 loop : 0.09 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 100 TYR 0.018 0.002 TYR D 91 PHE 0.016 0.002 PHE G 410 TRP 0.017 0.001 TRP H 178 HIS 0.005 0.001 HIS H 336 Details of bonding type rmsd covalent geometry : bond 0.00399 (19013) covalent geometry : angle 0.60104 (25809) SS BOND : bond 0.00300 ( 42) SS BOND : angle 0.79590 ( 84) hydrogen bonds : bond 0.04149 ( 592) hydrogen bonds : angle 6.72068 ( 1581) link_ALPHA1-2 : bond 0.00285 ( 4) link_ALPHA1-2 : angle 2.04582 ( 12) link_ALPHA1-3 : bond 0.00717 ( 8) link_ALPHA1-3 : angle 1.88035 ( 24) link_ALPHA1-6 : bond 0.00413 ( 8) link_ALPHA1-6 : angle 1.54519 ( 24) link_BETA1-4 : bond 0.00408 ( 47) link_BETA1-4 : angle 1.97579 ( 141) link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.32208 ( 72) *********************** 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 261 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 ASP cc_start: 0.8717 (m-30) cc_final: 0.8344 (t70) REVERT: H 150 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7759 (ttm110) REVERT: H 331 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8943 (p) REVERT: B 17 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 24 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: B 59 PRO cc_start: 0.9198 (Cg_exo) cc_final: 0.8919 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 81 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8471 (tm-30) REVERT: B 82 ASP cc_start: 0.9182 (m-30) cc_final: 0.8819 (m-30) REVERT: C 43 GLN cc_start: 0.8636 (mt0) cc_final: 0.8279 (mm-40) REVERT: C 89 GLU cc_start: 0.8946 (pm20) cc_final: 0.8670 (pm20) REVERT: C 98 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8034 (ttt-90) REVERT: D 59 PRO cc_start: 0.9076 (Cg_exo) cc_final: 0.8690 (Cg_endo) REVERT: I 23 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8200 (mtpm) REVERT: I 43 GLN cc_start: 0.7762 (mt0) cc_final: 0.7212 (mp10) REVERT: I 52 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8438 (mm) REVERT: I 73 ASP cc_start: 0.8204 (m-30) cc_final: 0.7985 (t0) REVERT: I 117 ASN cc_start: 0.8415 (m110) cc_final: 0.8152 (m110) REVERT: L 17 GLU cc_start: 0.7434 (mp0) cc_final: 0.6938 (mp0) REVERT: L 54 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8424 (mtm-85) REVERT: L 81 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8535 (mp0) REVERT: L 82 ASP cc_start: 0.8831 (m-30) cc_final: 0.8621 (m-30) REVERT: L 98 THR cc_start: 0.8961 (m) cc_final: 0.8625 (p) REVERT: A 23 LYS cc_start: 0.8468 (tttt) cc_final: 0.8205 (ttmt) REVERT: A 43 GLN cc_start: 0.8122 (mp10) cc_final: 0.7285 (mp10) REVERT: A 73 ASP cc_start: 0.8336 (m-30) cc_final: 0.7738 (t70) REVERT: A 111 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8500 (mm-30) outliers start: 29 outliers final: 9 residues processed: 244 average time/residue: 0.7222 time to fit residues: 193.8177 Evaluate side-chains 235 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 10 GLU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 41 optimal weight: 0.2980 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 F 141 ASN B 93 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.057779 restraints weight = 31498.580| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.42 r_work: 0.2629 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19146 Z= 0.177 Angle : 0.625 6.120 26166 Z= 0.314 Chirality : 0.045 0.207 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.356 56.563 4289 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Rotamer: Outliers : 1.13 % Allowed : 10.98 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2246 helix: -0.72 (0.83), residues: 28 sheet: -0.28 (0.17), residues: 847 loop : 0.12 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 100 TYR 0.018 0.002 TYR L 91 PHE 0.016 0.002 PHE G 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 347 Details of bonding type rmsd covalent geometry : bond 0.00387 (19013) covalent geometry : angle 0.59477 (25809) SS BOND : bond 0.00331 ( 42) SS BOND : angle 0.71077 ( 84) hydrogen bonds : bond 0.04057 ( 592) hydrogen bonds : angle 6.62303 ( 1581) link_ALPHA1-2 : bond 0.00280 ( 4) link_ALPHA1-2 : angle 2.02767 ( 12) link_ALPHA1-3 : bond 0.00672 ( 8) link_ALPHA1-3 : angle 1.87772 ( 24) link_ALPHA1-6 : bond 0.00428 ( 8) link_ALPHA1-6 : angle 1.55695 ( 24) link_BETA1-4 : bond 0.00398 ( 47) link_BETA1-4 : angle 1.81578 ( 141) link_NAG-ASN : bond 0.00356 ( 24) link_NAG-ASN : angle 2.29041 ( 72) *********************** 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 252 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9224 (tttt) cc_final: 0.8890 (ttpt) REVERT: G 93 ASP cc_start: 0.8715 (m-30) cc_final: 0.8366 (t70) REVERT: H 150 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7747 (ttm110) REVERT: H 331 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8951 (p) REVERT: B 17 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 24 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7904 (ttm-80) REVERT: B 59 PRO cc_start: 0.9185 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 81 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8485 (tm-30) REVERT: B 82 ASP cc_start: 0.9171 (m-30) cc_final: 0.8911 (m-30) REVERT: C 12 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8503 (mtpt) REVERT: C 43 GLN cc_start: 0.8606 (mt0) cc_final: 0.8243 (mm-40) REVERT: C 98 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (ttt-90) REVERT: D 17 GLU cc_start: 0.7684 (mp0) cc_final: 0.7375 (mp0) REVERT: D 33 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8338 (tm) REVERT: D 59 PRO cc_start: 0.9078 (Cg_exo) cc_final: 0.8693 (Cg_endo) REVERT: D 61 ARG cc_start: 0.8894 (ptp90) cc_final: 0.8496 (ptp90) REVERT: D 104 LYS cc_start: 0.8833 (tptm) cc_final: 0.8545 (tptp) REVERT: I 23 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8208 (mtpm) REVERT: I 43 GLN cc_start: 0.7734 (mt0) cc_final: 0.7216 (mp10) REVERT: I 52 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8441 (mm) REVERT: I 73 ASP cc_start: 0.8264 (m-30) cc_final: 0.8045 (t0) REVERT: I 117 ASN cc_start: 0.8379 (m110) cc_final: 0.8131 (m110) REVERT: L 17 GLU cc_start: 0.7453 (mp0) cc_final: 0.7041 (mp0) REVERT: L 45 ARG cc_start: 0.8349 (ttt-90) cc_final: 0.8002 (ttt180) REVERT: L 54 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: L 81 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8550 (mp0) REVERT: L 98 THR cc_start: 0.8959 (m) cc_final: 0.8650 (p) REVERT: A 23 LYS cc_start: 0.8465 (tttt) cc_final: 0.8192 (ttmt) REVERT: A 43 GLN cc_start: 0.8113 (mp10) cc_final: 0.7281 (mp10) REVERT: A 63 LYS cc_start: 0.9398 (mtpp) cc_final: 0.8971 (ptmm) REVERT: A 73 ASP cc_start: 0.8332 (m-30) cc_final: 0.7766 (t70) outliers start: 22 outliers final: 6 residues processed: 238 average time/residue: 0.7027 time to fit residues: 183.8727 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 222 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 C residue 98 ARG 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 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 141 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN G 465 ASN H 465 ASN B 6 GLN B 93 ASN A 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 = 0.3209 r_free = 0.3209 target = 0.080721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057151 restraints weight = 31872.413| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.44 r_work: 0.2615 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2449 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= 0.206 Angle : 0.631 6.498 26166 Z= 0.317 Chirality : 0.046 0.211 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.359 59.428 4289 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 1.08 % Allowed : 11.03 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2246 helix: -0.67 (0.83), residues: 28 sheet: -0.28 (0.17), residues: 847 loop : 0.11 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 100 TYR 0.024 0.002 TYR L 91 PHE 0.017 0.002 PHE G 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00454 (19013) covalent geometry : angle 0.60134 (25809) SS BOND : bond 0.00341 ( 42) SS BOND : angle 0.70882 ( 84) hydrogen bonds : bond 0.04187 ( 592) hydrogen bonds : angle 6.63418 ( 1581) link_ALPHA1-2 : bond 0.00203 ( 4) link_ALPHA1-2 : angle 2.04856 ( 12) link_ALPHA1-3 : bond 0.00546 ( 8) link_ALPHA1-3 : angle 1.95792 ( 24) link_ALPHA1-6 : bond 0.00349 ( 8) link_ALPHA1-6 : angle 1.60011 ( 24) link_BETA1-4 : bond 0.00383 ( 47) link_BETA1-4 : angle 1.71961 ( 141) link_NAG-ASN : bond 0.00436 ( 24) link_NAG-ASN : angle 2.37904 ( 72) *********************** 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 249 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9241 (tttt) cc_final: 0.8905 (ttpt) REVERT: G 93 ASP cc_start: 0.8721 (m-30) cc_final: 0.8408 (t70) REVERT: H 150 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7751 (ttm110) REVERT: H 331 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 17 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 24 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7891 (ttm-80) REVERT: B 59 PRO cc_start: 0.9202 (Cg_exo) cc_final: 0.8897 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 81 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8406 (tm-30) REVERT: B 82 ASP cc_start: 0.9178 (m-30) cc_final: 0.8798 (m-30) REVERT: B 104 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8779 (tppp) REVERT: C 12 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8447 (mtpt) REVERT: C 43 GLN cc_start: 0.8589 (mt0) cc_final: 0.8219 (mm-40) REVERT: C 98 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8095 (ttt-90) REVERT: D 17 GLU cc_start: 0.7733 (mp0) cc_final: 0.7380 (mp0) REVERT: D 33 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8338 (tm) REVERT: D 61 ARG cc_start: 0.8879 (ptp90) cc_final: 0.8515 (ptp90) REVERT: D 104 LYS cc_start: 0.8836 (tptm) cc_final: 0.8535 (tptp) REVERT: I 23 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8205 (mtpm) REVERT: I 38 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7341 (ptt180) REVERT: I 43 GLN cc_start: 0.7728 (mt0) cc_final: 0.7248 (mp10) REVERT: I 52 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8437 (mm) REVERT: I 73 ASP cc_start: 0.8292 (m-30) cc_final: 0.8063 (t0) REVERT: I 117 ASN cc_start: 0.8381 (m110) cc_final: 0.8116 (m110) REVERT: L 17 GLU cc_start: 0.7454 (mp0) cc_final: 0.7020 (mp0) REVERT: L 45 ARG cc_start: 0.8334 (ttt-90) cc_final: 0.7991 (ttt180) REVERT: L 54 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8444 (mtm-85) REVERT: L 81 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8550 (mp0) REVERT: L 98 THR cc_start: 0.9037 (m) cc_final: 0.8688 (p) REVERT: A 23 LYS cc_start: 0.8487 (tttt) cc_final: 0.8220 (ttmt) REVERT: A 43 GLN cc_start: 0.8104 (mp10) cc_final: 0.7538 (mp10) REVERT: A 63 LYS cc_start: 0.9371 (mtpp) cc_final: 0.9109 (ptpp) outliers start: 21 outliers final: 6 residues processed: 238 average time/residue: 0.6764 time to fit residues: 177.2327 Evaluate side-chains 232 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain C residue 98 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 192 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.058720 restraints weight = 31614.440| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.43 r_work: 0.2650 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19146 Z= 0.153 Angle : 0.605 6.639 26166 Z= 0.305 Chirality : 0.045 0.206 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.029 55.499 4289 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 0.82 % Allowed : 11.65 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.18), residues: 2246 helix: -0.67 (0.83), residues: 28 sheet: -0.35 (0.17), residues: 863 loop : 0.24 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 100 TYR 0.021 0.002 TYR L 91 PHE 0.015 0.002 PHE F 410 TRP 0.016 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00332 (19013) covalent geometry : angle 0.57989 (25809) SS BOND : bond 0.00256 ( 42) SS BOND : angle 0.65806 ( 84) hydrogen bonds : bond 0.03850 ( 592) hydrogen bonds : angle 6.49199 ( 1581) link_ALPHA1-2 : bond 0.00340 ( 4) link_ALPHA1-2 : angle 1.97229 ( 12) link_ALPHA1-3 : bond 0.00809 ( 8) link_ALPHA1-3 : angle 1.77735 ( 24) link_ALPHA1-6 : bond 0.00488 ( 8) link_ALPHA1-6 : angle 1.51942 ( 24) link_BETA1-4 : bond 0.00404 ( 47) link_BETA1-4 : angle 1.57328 ( 141) link_NAG-ASN : bond 0.00288 ( 24) link_NAG-ASN : angle 2.15495 ( 72) *********************** 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 253 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9237 (tttt) cc_final: 0.8888 (ttpt) REVERT: G 93 ASP cc_start: 0.8734 (m-30) cc_final: 0.8449 (t70) REVERT: G 381 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8395 (mt-10) REVERT: H 150 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7723 (ttm110) REVERT: B 17 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 24 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7862 (ttm-80) REVERT: B 59 PRO cc_start: 0.9188 (Cg_exo) cc_final: 0.8906 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 81 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8336 (tm-30) REVERT: B 104 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8766 (tppp) REVERT: C 10 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: C 12 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8496 (mtpt) REVERT: C 23 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8331 (mmmt) REVERT: C 43 GLN cc_start: 0.8588 (mt0) cc_final: 0.8217 (mm-40) REVERT: C 98 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8074 (ttt-90) REVERT: D 17 GLU cc_start: 0.7744 (mp0) cc_final: 0.7461 (mp0) REVERT: D 33 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8240 (tm) REVERT: D 59 PRO cc_start: 0.9115 (Cg_exo) cc_final: 0.8739 (Cg_endo) REVERT: D 61 ARG cc_start: 0.8860 (ptp90) cc_final: 0.8490 (ptp90) REVERT: I 23 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8227 (mtpm) REVERT: I 43 GLN cc_start: 0.7699 (mt0) cc_final: 0.7197 (mp10) REVERT: I 73 ASP cc_start: 0.8277 (m-30) cc_final: 0.8038 (t0) REVERT: I 117 ASN cc_start: 0.8373 (m110) cc_final: 0.8155 (m110) REVERT: L 17 GLU cc_start: 0.7456 (mp0) cc_final: 0.7015 (mp0) REVERT: L 45 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8028 (ttt180) REVERT: L 54 ARG cc_start: 0.8853 (mtm-85) cc_final: 0.8438 (mtm-85) REVERT: L 81 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8529 (mp0) REVERT: L 98 THR cc_start: 0.9046 (m) cc_final: 0.8708 (p) REVERT: A 13 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.7902 (mtp85) REVERT: A 23 LYS cc_start: 0.8529 (tttt) cc_final: 0.8275 (ttmt) REVERT: A 43 GLN cc_start: 0.8131 (mp10) cc_final: 0.7565 (mp10) REVERT: A 63 LYS cc_start: 0.9360 (mtpp) cc_final: 0.9080 (ptmm) REVERT: A 67 ARG cc_start: 0.8825 (ptt90) cc_final: 0.8533 (ptt90) REVERT: A 73 ASP cc_start: 0.8396 (m-30) cc_final: 0.7218 (p0) outliers start: 16 outliers final: 4 residues processed: 243 average time/residue: 0.7020 time to fit residues: 187.4193 Evaluate side-chains 232 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 104 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 152 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 175 optimal weight: 0.0070 chunk 136 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN F 141 ASN B 93 ASN A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.057499 restraints weight = 31887.207| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.43 r_work: 0.2621 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19146 Z= 0.207 Angle : 0.625 6.877 26166 Z= 0.315 Chirality : 0.045 0.215 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.113 54.728 4289 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 0.93 % Allowed : 11.75 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.18), residues: 2246 helix: -0.56 (0.85), residues: 28 sheet: -0.28 (0.17), residues: 855 loop : 0.20 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 100 TYR 0.022 0.002 TYR L 91 PHE 0.017 0.002 PHE G 410 TRP 0.015 0.001 TRP H 178 HIS 0.003 0.001 HIS H 336 Details of bonding type rmsd covalent geometry : bond 0.00458 (19013) covalent geometry : angle 0.59793 (25809) SS BOND : bond 0.00340 ( 42) SS BOND : angle 0.69883 ( 84) hydrogen bonds : bond 0.04145 ( 592) hydrogen bonds : angle 6.56784 ( 1581) link_ALPHA1-2 : bond 0.00195 ( 4) link_ALPHA1-2 : angle 2.02190 ( 12) link_ALPHA1-3 : bond 0.00587 ( 8) link_ALPHA1-3 : angle 1.98952 ( 24) link_ALPHA1-6 : bond 0.00350 ( 8) link_ALPHA1-6 : angle 1.61285 ( 24) link_BETA1-4 : bond 0.00380 ( 47) link_BETA1-4 : angle 1.59137 ( 141) link_NAG-ASN : bond 0.00451 ( 24) link_NAG-ASN : angle 2.35297 ( 72) *********************** 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 242 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9234 (tttt) cc_final: 0.8881 (ttpt) REVERT: G 93 ASP cc_start: 0.8735 (m-30) cc_final: 0.8444 (t70) REVERT: G 381 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8401 (mt-10) REVERT: H 150 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7739 (ttm110) REVERT: H 331 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 17 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 24 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7867 (ttm-80) REVERT: B 59 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8907 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 81 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8268 (tm-30) REVERT: B 104 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8779 (tppp) REVERT: C 10 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: C 12 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8498 (mtpt) REVERT: C 23 LYS cc_start: 0.8572 (mtpm) cc_final: 0.8341 (mmmt) REVERT: C 43 GLN cc_start: 0.8600 (mt0) cc_final: 0.8220 (mm-40) REVERT: C 98 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: D 17 GLU cc_start: 0.7726 (mp0) cc_final: 0.7408 (mp0) REVERT: D 33 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8314 (tm) REVERT: D 61 ARG cc_start: 0.8857 (ptp90) cc_final: 0.8508 (ptp90) REVERT: I 23 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8211 (mtpm) REVERT: I 38 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7903 (ptt180) REVERT: I 43 GLN cc_start: 0.7723 (mt0) cc_final: 0.7227 (mp10) REVERT: I 73 ASP cc_start: 0.8298 (m-30) cc_final: 0.8037 (t0) REVERT: I 117 ASN cc_start: 0.8420 (m110) cc_final: 0.8197 (m110) REVERT: L 17 GLU cc_start: 0.7422 (mp0) cc_final: 0.6970 (mp0) REVERT: L 45 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.8025 (ttt180) REVERT: L 54 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8412 (mtm-85) REVERT: L 81 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8557 (mp0) REVERT: L 98 THR cc_start: 0.9056 (m) cc_final: 0.8738 (p) REVERT: A 13 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.7920 (mtp85) REVERT: A 23 LYS cc_start: 0.8499 (tttt) cc_final: 0.8242 (ttmt) REVERT: A 43 GLN cc_start: 0.8087 (mp10) cc_final: 0.7587 (mp10) REVERT: A 63 LYS cc_start: 0.9358 (mtpp) cc_final: 0.9137 (ptpp) REVERT: A 67 ARG cc_start: 0.8819 (ptt90) cc_final: 0.8532 (ptt90) REVERT: A 73 ASP cc_start: 0.8386 (m-30) cc_final: 0.7313 (p0) outliers start: 18 outliers final: 5 residues processed: 232 average time/residue: 0.7401 time to fit residues: 188.7497 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 98 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 95 optimal weight: 0.0970 chunk 193 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.059979 restraints weight = 31482.816| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.46 r_work: 0.2679 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19146 Z= 0.127 Angle : 0.591 7.503 26166 Z= 0.299 Chirality : 0.045 0.202 3085 Planarity : 0.004 0.042 3191 Dihedral : 6.678 48.527 4289 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 0.46 % Allowed : 12.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2246 helix: -0.58 (0.85), residues: 28 sheet: -0.29 (0.17), residues: 863 loop : 0.29 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 54 TYR 0.018 0.002 TYR B 91 PHE 0.014 0.002 PHE F 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00274 (19013) covalent geometry : angle 0.56936 (25809) SS BOND : bond 0.00220 ( 42) SS BOND : angle 0.58547 ( 84) hydrogen bonds : bond 0.03672 ( 592) hydrogen bonds : angle 6.37082 ( 1581) link_ALPHA1-2 : bond 0.00422 ( 4) link_ALPHA1-2 : angle 1.90879 ( 12) link_ALPHA1-3 : bond 0.00912 ( 8) link_ALPHA1-3 : angle 1.65403 ( 24) link_ALPHA1-6 : bond 0.00558 ( 8) link_ALPHA1-6 : angle 1.48663 ( 24) link_BETA1-4 : bond 0.00427 ( 47) link_BETA1-4 : angle 1.45933 ( 141) link_NAG-ASN : bond 0.00211 ( 24) link_NAG-ASN : angle 2.02845 ( 72) ********************** 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 240 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9232 (tttt) cc_final: 0.8877 (ttpt) REVERT: G 93 ASP cc_start: 0.8706 (m-30) cc_final: 0.8445 (t70) REVERT: G 381 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8357 (mt-10) REVERT: H 150 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7741 (ttm110) REVERT: B 17 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8327 (mm-30) REVERT: B 24 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7852 (ttm-80) REVERT: B 70 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 91 TYR cc_start: 0.8829 (p90) cc_final: 0.8524 (p90) REVERT: B 104 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8751 (tppp) REVERT: C 23 LYS cc_start: 0.8569 (mtpm) cc_final: 0.8365 (mmmt) REVERT: C 43 GLN cc_start: 0.8610 (mt0) cc_final: 0.8198 (mm-40) REVERT: C 54 THR cc_start: 0.9234 (m) cc_final: 0.8966 (p) REVERT: C 98 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8081 (ttt-90) REVERT: D 17 GLU cc_start: 0.7725 (mp0) cc_final: 0.7386 (mp0) REVERT: D 33 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8212 (tm) REVERT: D 59 PRO cc_start: 0.9128 (Cg_exo) cc_final: 0.8757 (Cg_endo) REVERT: D 61 ARG cc_start: 0.8856 (ptp90) cc_final: 0.8498 (ptp90) REVERT: I 23 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8217 (mtpm) REVERT: I 43 GLN cc_start: 0.7733 (mt0) cc_final: 0.7270 (mp10) REVERT: I 73 ASP cc_start: 0.8284 (m-30) cc_final: 0.8034 (t0) REVERT: L 17 GLU cc_start: 0.7399 (mp0) cc_final: 0.6763 (mp0) REVERT: L 45 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8054 (ttt180) REVERT: L 54 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: L 81 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8572 (mp0) REVERT: L 98 THR cc_start: 0.9062 (m) cc_final: 0.8766 (p) REVERT: A 13 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.7899 (mtp85) REVERT: A 43 GLN cc_start: 0.8083 (mp10) cc_final: 0.7594 (mp10) REVERT: A 63 LYS cc_start: 0.9328 (mtpp) cc_final: 0.9121 (ptmm) REVERT: A 67 ARG cc_start: 0.8832 (ptt90) cc_final: 0.8198 (ptt90) REVERT: A 73 ASP cc_start: 0.8336 (m-30) cc_final: 0.7248 (p0) REVERT: A 78 THR cc_start: 0.8116 (m) cc_final: 0.7278 (t) REVERT: A 87 ARG cc_start: 0.7511 (mpt-90) cc_final: 0.7300 (mpt-90) outliers start: 9 outliers final: 4 residues processed: 236 average time/residue: 0.7451 time to fit residues: 193.8841 Evaluate side-chains 231 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 104 LYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER 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 121 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN F 141 ASN A 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.059820 restraints weight = 31713.432| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.44 r_work: 0.2677 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 19146 Z= 0.173 Angle : 0.771 59.199 26166 Z= 0.422 Chirality : 0.045 0.254 3085 Planarity : 0.004 0.042 3191 Dihedral : 6.677 48.538 4289 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.57 % Allowed : 12.94 % Favored : 86.49 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2246 helix: -0.59 (0.84), residues: 28 sheet: -0.29 (0.17), residues: 863 loop : 0.29 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE F 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00367 (19013) covalent geometry : angle 0.75662 (25809) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.56610 ( 84) hydrogen bonds : bond 0.03673 ( 592) hydrogen bonds : angle 6.37054 ( 1581) link_ALPHA1-2 : bond 0.00440 ( 4) link_ALPHA1-2 : angle 1.91604 ( 12) link_ALPHA1-3 : bond 0.00912 ( 8) link_ALPHA1-3 : angle 1.65068 ( 24) link_ALPHA1-6 : bond 0.00561 ( 8) link_ALPHA1-6 : angle 1.48886 ( 24) link_BETA1-4 : bond 0.00453 ( 47) link_BETA1-4 : angle 1.46384 ( 141) link_NAG-ASN : bond 0.00216 ( 24) link_NAG-ASN : angle 2.02515 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7422.97 seconds wall clock time: 127 minutes 26.80 seconds (7646.80 seconds total)