Starting phenix.real_space_refine on Tue May 20 21:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3p_29707/05_2025/8g3p_29707.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12560 2.51 5 N 3448 2.21 5 O 4192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 40 Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "E" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} 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: "q" 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: "r" 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "M" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "b" 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: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "U" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "X" 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: "d" 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: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.92, per 1000 atoms: 0.64 Number of scatterers: 20321 At special positions: 0 Unit cell: (166.83, 166.83, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4192 8.00 N 3448 7.00 C 12560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.08 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.06 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=1.99 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.07 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.09 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.09 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.14 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.08 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.06 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=1.99 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.07 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.07 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.09 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.07 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.09 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.08 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=1.99 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.07 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.07 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.09 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.07 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.09 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.08 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.06 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.99 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.07 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=2.09 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.07 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.09 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.14 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 S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " 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 U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG M 1 " - " ASN A 86 " " NAG N 1 " - " ASN D 86 " " NAG O 1 " - " ASN E 86 " " NAG P 1 " - " ASN A 146 " " NAG Q 1 " - " ASN D 146 " " NAG R 1 " - " ASN E 146 " " NAG S 1 " - " ASN A 200 " " NAG T 1 " - " ASN D 200 " " NAG U 1 " - " ASN E 200 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN A 245 " " NAG Z 1 " - " ASN D 245 " " NAG a 1 " - " ASN E 245 " " NAG b 1 " - " ASN A 367 " " NAG c 1 " - " ASN D 367 " " NAG d 1 " - " ASN E 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.747A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.738A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.741A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.737A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.786A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 117 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.570A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.558A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.788A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP A 197 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.613A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP D 197 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.621A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.047A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 363 " --> pdb=" O TRP E 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.77 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3493 1.32 - 1.44: 5751 1.44 - 1.57: 11360 1.57 - 1.69: 4 1.69 - 1.82: 144 Bond restraints: 20752 Sorted by residual: bond pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" N ILE E 176 " pdb=" CA ILE E 176 " ideal model delta sigma weight residual 1.460 1.507 -0.048 1.10e-02 8.26e+03 1.89e+01 bond pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C GLU B 162 " pdb=" O GLU B 162 " ideal model delta sigma weight residual 1.234 1.283 -0.049 1.24e-02 6.50e+03 1.59e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21327 1.82 - 3.64: 5946 3.64 - 5.46: 766 5.46 - 7.28: 113 7.28 - 9.11: 16 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE D 397 " pdb=" CA ILE D 397 " pdb=" C ILE D 397 " ideal model delta sigma weight residual 111.67 106.32 5.35 9.50e-01 1.11e+00 3.17e+01 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 111.67 106.35 5.32 9.50e-01 1.11e+00 3.14e+01 angle pdb=" CA ASP B 125 " pdb=" CB ASP B 125 " pdb=" CG ASP B 125 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.91e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 12481 19.63 - 39.26: 539 39.26 - 58.90: 116 58.90 - 78.53: 52 78.53 - 98.16: 40 Dihedral angle restraints: 13228 sinusoidal: 6092 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASN E 441 " pdb=" C ASN E 441 " pdb=" N SER E 442 " pdb=" CA SER E 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN B 441 " pdb=" C ASN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN D 441 " pdb=" C ASN D 441 " pdb=" N SER D 442 " pdb=" CA SER D 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 13225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2162 0.091 - 0.182: 1018 0.182 - 0.273: 92 0.273 - 0.364: 8 0.364 - 0.454: 12 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.79e+01 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.64e+01 ... (remaining 3289 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 281 " -0.084 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR D 281 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 281 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR D 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR D 281 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 281 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 281 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 281 " 0.085 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR B 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 281 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.085 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR E 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4924 2.83 - 3.35: 19156 3.35 - 3.87: 36030 3.87 - 4.38: 44702 4.38 - 4.90: 72604 Nonbonded interactions: 177416 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP B 293 " pdb="CA CA B2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D2000 " model vdw 2.316 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.316 2.510 nonbonded pdb=" O HIS D 347 " pdb="CA CA D2000 " model vdw 2.317 2.510 ... (remaining 177411 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 'A' and (resid 82 through 469 or resid 501)) selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'u' } 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.430 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.170 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 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 : 0.015 0.107 20872 Z= 1.012 Angle : 1.682 12.309 28484 Z= 1.066 Chirality : 0.094 0.454 3292 Planarity : 0.010 0.071 3528 Dihedral : 13.928 98.160 8552 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2488 helix: -0.11 (0.97), residues: 24 sheet: -0.04 (0.16), residues: 1008 loop : -0.81 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.012 TRP J 97 HIS 0.021 0.006 HIS A 168 PHE 0.060 0.013 PHE E 205 TYR 0.085 0.013 TYR B 281 ARG 0.019 0.003 ARG E 224 Details of bonding type rmsd link_NAG-ASN : bond 0.01036 ( 24) link_NAG-ASN : angle 5.47149 ( 72) link_ALPHA1-6 : bond 0.01189 ( 8) link_ALPHA1-6 : angle 2.42299 ( 24) link_BETA1-4 : bond 0.01430 ( 28) link_BETA1-4 : angle 4.56298 ( 84) link_ALPHA1-2 : bond 0.00807 ( 4) link_ALPHA1-2 : angle 4.60407 ( 12) link_ALPHA1-3 : bond 0.00989 ( 8) link_ALPHA1-3 : angle 2.54638 ( 24) hydrogen bonds : bond 0.15070 ( 640) hydrogen bonds : angle 8.49030 ( 1680) link_BETA1-6 : bond 0.01042 ( 4) link_BETA1-6 : angle 3.14322 ( 12) SS BOND : bond 0.05062 ( 44) SS BOND : angle 2.33670 ( 88) covalent geometry : bond 0.01455 (20752) covalent geometry : angle 1.63736 (28168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.9335 (ttmt) cc_final: 0.9135 (mtpm) REVERT: I 70 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 400 ARG cc_start: 0.9264 (ptm-80) cc_final: 0.9027 (ptm160) REVERT: F 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: J 70 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9029 (ptm160) REVERT: G 23 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9133 (mtpm) REVERT: K 70 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9028 (ptm160) REVERT: H 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: L 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7811 (mt-10) REVERT: E 400 ARG cc_start: 0.9265 (ptm-80) cc_final: 0.9026 (ptm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.6776 time to fit residues: 539.7603 Evaluate side-chains 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS F 32 GLN F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS G 32 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS H 32 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054913 restraints weight = 37481.469| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.64 r_work: 0.2620 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 20872 Z= 0.165 Angle : 0.702 8.614 28484 Z= 0.365 Chirality : 0.047 0.262 3292 Planarity : 0.004 0.045 3528 Dihedral : 8.876 73.503 4260 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 1.69 % Allowed : 6.88 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2488 helix: 0.27 (0.88), residues: 24 sheet: -0.05 (0.15), residues: 1068 loop : -0.27 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 178 HIS 0.003 0.001 HIS A 168 PHE 0.014 0.002 PHE D 410 TYR 0.013 0.002 TYR C 95 ARG 0.008 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 24) link_NAG-ASN : angle 3.00153 ( 72) link_ALPHA1-6 : bond 0.00571 ( 8) link_ALPHA1-6 : angle 1.34514 ( 24) link_BETA1-4 : bond 0.00333 ( 28) link_BETA1-4 : angle 2.24088 ( 84) link_ALPHA1-2 : bond 0.00533 ( 4) link_ALPHA1-2 : angle 1.89218 ( 12) link_ALPHA1-3 : bond 0.00948 ( 8) link_ALPHA1-3 : angle 1.84637 ( 24) hydrogen bonds : bond 0.04733 ( 640) hydrogen bonds : angle 7.07422 ( 1680) link_BETA1-6 : bond 0.00492 ( 4) link_BETA1-6 : angle 1.27790 ( 12) SS BOND : bond 0.00302 ( 44) SS BOND : angle 0.60189 ( 88) covalent geometry : bond 0.00366 (20752) covalent geometry : angle 0.67281 (28168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8522 (mtpm) REVERT: I 17 GLU cc_start: 0.7725 (mp0) cc_final: 0.7452 (mp0) REVERT: I 24 ARG cc_start: 0.7669 (ttm110) cc_final: 0.6890 (ttm110) REVERT: I 81 GLU cc_start: 0.8887 (pm20) cc_final: 0.8629 (pp20) REVERT: B 400 ARG cc_start: 0.8632 (ptm-80) cc_final: 0.8331 (ptm160) REVERT: F 23 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8511 (mtpm) REVERT: J 17 GLU cc_start: 0.7724 (mp0) cc_final: 0.7450 (mp0) REVERT: J 24 ARG cc_start: 0.7668 (ttm110) cc_final: 0.6890 (ttm110) REVERT: J 81 GLU cc_start: 0.8894 (pm20) cc_final: 0.8630 (pp20) REVERT: A 400 ARG cc_start: 0.8652 (ptm-80) cc_final: 0.8337 (ptm160) REVERT: G 23 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8516 (mtpm) REVERT: K 17 GLU cc_start: 0.7720 (mp0) cc_final: 0.7447 (mp0) REVERT: K 24 ARG cc_start: 0.7668 (ttm110) cc_final: 0.6897 (ttm110) REVERT: K 81 GLU cc_start: 0.8893 (pm20) cc_final: 0.8595 (pp20) REVERT: D 400 ARG cc_start: 0.8650 (ptm-80) cc_final: 0.8337 (ptm160) REVERT: H 23 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8516 (mtpm) REVERT: L 17 GLU cc_start: 0.7720 (mp0) cc_final: 0.7447 (mp0) REVERT: L 24 ARG cc_start: 0.7672 (ttm110) cc_final: 0.6853 (ttm110) REVERT: L 81 GLU cc_start: 0.8894 (pm20) cc_final: 0.8640 (pp20) REVERT: E 400 ARG cc_start: 0.8631 (ptm-80) cc_final: 0.8330 (ptm160) outliers start: 36 outliers final: 12 residues processed: 245 average time/residue: 1.5875 time to fit residues: 432.0525 Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 41 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 243 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 468 HIS H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.055308 restraints weight = 37418.337| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.60 r_work: 0.2635 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20872 Z= 0.145 Angle : 0.641 7.442 28484 Z= 0.334 Chirality : 0.046 0.250 3292 Planarity : 0.003 0.030 3528 Dihedral : 8.006 63.804 4260 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 1.54 % Allowed : 8.75 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2488 helix: 0.07 (0.79), residues: 24 sheet: -0.08 (0.15), residues: 1068 loop : -0.22 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 178 HIS 0.004 0.001 HIS D 468 PHE 0.015 0.002 PHE D 410 TYR 0.014 0.001 TYR D 121 ARG 0.008 0.001 ARG J 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 24) link_NAG-ASN : angle 2.56009 ( 72) link_ALPHA1-6 : bond 0.00547 ( 8) link_ALPHA1-6 : angle 1.32782 ( 24) link_BETA1-4 : bond 0.00417 ( 28) link_BETA1-4 : angle 1.95401 ( 84) link_ALPHA1-2 : bond 0.00720 ( 4) link_ALPHA1-2 : angle 2.07439 ( 12) link_ALPHA1-3 : bond 0.00995 ( 8) link_ALPHA1-3 : angle 1.64710 ( 24) hydrogen bonds : bond 0.04202 ( 640) hydrogen bonds : angle 6.71024 ( 1680) link_BETA1-6 : bond 0.00377 ( 4) link_BETA1-6 : angle 1.40105 ( 12) SS BOND : bond 0.00230 ( 44) SS BOND : angle 0.39929 ( 88) covalent geometry : bond 0.00323 (20752) covalent geometry : angle 0.61664 (28168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8469 (mtpm) REVERT: I 17 GLU cc_start: 0.7848 (mp0) cc_final: 0.7560 (mp0) REVERT: I 24 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7373 (ttm110) REVERT: I 70 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6835 (mm-30) REVERT: I 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8616 (pp20) REVERT: I 107 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.6961 (mm) REVERT: B 400 ARG cc_start: 0.8666 (ptm-80) cc_final: 0.8333 (ptm160) REVERT: F 23 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8467 (mtpm) REVERT: J 17 GLU cc_start: 0.7833 (mp0) cc_final: 0.7538 (mp0) REVERT: J 24 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7378 (ttm110) REVERT: J 70 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6836 (mm-30) REVERT: J 81 GLU cc_start: 0.8907 (pm20) cc_final: 0.8627 (pp20) REVERT: J 107 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.6954 (mm) REVERT: A 400 ARG cc_start: 0.8662 (ptm-80) cc_final: 0.8331 (ptm160) REVERT: G 23 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8461 (mtpm) REVERT: G 46 GLU cc_start: 0.8039 (tt0) cc_final: 0.7562 (tt0) REVERT: G 63 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8120 (mtp-110) REVERT: K 17 GLU cc_start: 0.7845 (mp0) cc_final: 0.7553 (mp0) REVERT: K 24 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7305 (ttm110) REVERT: K 70 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6829 (mm-30) REVERT: K 81 GLU cc_start: 0.8900 (pm20) cc_final: 0.8616 (pp20) REVERT: K 107 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7040 (mm) REVERT: D 400 ARG cc_start: 0.8660 (ptm-80) cc_final: 0.8327 (ptm160) REVERT: H 23 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8475 (mtpm) REVERT: H 90 ASP cc_start: 0.7605 (m-30) cc_final: 0.7099 (m-30) REVERT: L 17 GLU cc_start: 0.7843 (mp0) cc_final: 0.7552 (mp0) REVERT: L 24 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7215 (ttm110) REVERT: L 70 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6831 (mm-30) REVERT: L 81 GLU cc_start: 0.8897 (pm20) cc_final: 0.8627 (pp20) REVERT: L 107 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.6961 (mm) REVERT: E 400 ARG cc_start: 0.8654 (ptm-80) cc_final: 0.8321 (ptm160) outliers start: 33 outliers final: 16 residues processed: 229 average time/residue: 1.6962 time to fit residues: 428.4031 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 91 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 468 HIS A 274 HIS A 468 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 274 HIS E 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.055062 restraints weight = 37694.711| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.62 r_work: 0.2630 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20872 Z= 0.154 Angle : 0.619 7.068 28484 Z= 0.320 Chirality : 0.045 0.249 3292 Planarity : 0.004 0.038 3528 Dihedral : 7.600 58.126 4260 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.78 % Rotamer: Outliers : 1.31 % Allowed : 9.69 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2488 helix: -0.09 (0.75), residues: 24 sheet: -0.16 (0.15), residues: 1088 loop : -0.11 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.003 0.001 HIS A 468 PHE 0.014 0.002 PHE E 410 TYR 0.013 0.001 TYR D 121 ARG 0.008 0.000 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 24) link_NAG-ASN : angle 2.45686 ( 72) link_ALPHA1-6 : bond 0.00497 ( 8) link_ALPHA1-6 : angle 1.36410 ( 24) link_BETA1-4 : bond 0.00380 ( 28) link_BETA1-4 : angle 1.85094 ( 84) link_ALPHA1-2 : bond 0.00652 ( 4) link_ALPHA1-2 : angle 2.12585 ( 12) link_ALPHA1-3 : bond 0.00884 ( 8) link_ALPHA1-3 : angle 1.74700 ( 24) hydrogen bonds : bond 0.04008 ( 640) hydrogen bonds : angle 6.47002 ( 1680) link_BETA1-6 : bond 0.00197 ( 4) link_BETA1-6 : angle 1.56942 ( 12) SS BOND : bond 0.00258 ( 44) SS BOND : angle 0.54359 ( 88) covalent geometry : bond 0.00344 (20752) covalent geometry : angle 0.59523 (28168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8467 (mtpm) REVERT: C 46 GLU cc_start: 0.8035 (tt0) cc_final: 0.7624 (tt0) REVERT: C 63 ARG cc_start: 0.8508 (mtp-110) cc_final: 0.8111 (mtp-110) REVERT: C 65 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7704 (tp-100) REVERT: I 17 GLU cc_start: 0.7878 (mp0) cc_final: 0.7558 (mp0) REVERT: I 24 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7373 (ttm110) REVERT: I 79 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7615 (mp-120) REVERT: I 81 GLU cc_start: 0.8883 (pm20) cc_final: 0.8630 (pp20) REVERT: I 107 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7009 (mm) REVERT: B 400 ARG cc_start: 0.8661 (ptm-80) cc_final: 0.8345 (ptm160) REVERT: F 23 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8462 (mtpm) REVERT: F 46 GLU cc_start: 0.8044 (tt0) cc_final: 0.7694 (tt0) REVERT: F 63 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.8147 (mtp-110) REVERT: J 17 GLU cc_start: 0.7866 (mp0) cc_final: 0.7549 (mp0) REVERT: J 24 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7348 (ttm110) REVERT: J 79 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7612 (mp-120) REVERT: J 81 GLU cc_start: 0.8884 (pm20) cc_final: 0.8631 (pp20) REVERT: J 107 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.6999 (mm) REVERT: A 400 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8340 (ptm160) REVERT: G 23 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8456 (mtpm) REVERT: G 46 GLU cc_start: 0.8055 (tt0) cc_final: 0.7588 (tt0) REVERT: G 63 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8100 (mtp-110) REVERT: K 17 GLU cc_start: 0.7864 (mp0) cc_final: 0.7544 (mp0) REVERT: K 24 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7369 (ttm110) REVERT: K 79 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7605 (mp-120) REVERT: K 81 GLU cc_start: 0.8882 (pm20) cc_final: 0.8629 (pp20) REVERT: K 107 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.6999 (mm) REVERT: D 400 ARG cc_start: 0.8655 (ptm-80) cc_final: 0.8340 (ptm160) REVERT: H 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8465 (mtpm) REVERT: H 46 GLU cc_start: 0.8072 (tt0) cc_final: 0.7638 (tt0) REVERT: H 63 ARG cc_start: 0.8581 (mtp-110) cc_final: 0.8202 (mtp-110) REVERT: L 4 MET cc_start: 0.8512 (mmm) cc_final: 0.8262 (mmm) REVERT: L 17 GLU cc_start: 0.7885 (mp0) cc_final: 0.7567 (mp0) REVERT: L 24 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7330 (ttm110) REVERT: L 79 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7616 (mp-120) REVERT: L 81 GLU cc_start: 0.8884 (pm20) cc_final: 0.8638 (pp20) REVERT: L 107 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7001 (mm) REVERT: E 400 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.8330 (ptm160) outliers start: 28 outliers final: 20 residues processed: 224 average time/residue: 1.5969 time to fit residues: 398.0556 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 65 GLN B 468 HIS F 32 GLN A 468 HIS G 32 GLN D 468 HIS H 32 GLN E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.052899 restraints weight = 37835.403| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.62 r_work: 0.2578 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20872 Z= 0.269 Angle : 0.682 7.325 28484 Z= 0.353 Chirality : 0.048 0.262 3292 Planarity : 0.004 0.044 3528 Dihedral : 7.932 61.595 4260 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 1.31 % Allowed : 11.14 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2488 helix: -0.04 (0.77), residues: 24 sheet: -0.25 (0.15), residues: 1080 loop : -0.12 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 178 HIS 0.003 0.001 HIS E 168 PHE 0.015 0.002 PHE B 410 TYR 0.017 0.002 TYR E 121 ARG 0.011 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 24) link_NAG-ASN : angle 2.67991 ( 72) link_ALPHA1-6 : bond 0.00293 ( 8) link_ALPHA1-6 : angle 1.43119 ( 24) link_BETA1-4 : bond 0.00248 ( 28) link_BETA1-4 : angle 1.99907 ( 84) link_ALPHA1-2 : bond 0.00336 ( 4) link_ALPHA1-2 : angle 2.12665 ( 12) link_ALPHA1-3 : bond 0.00692 ( 8) link_ALPHA1-3 : angle 1.97664 ( 24) hydrogen bonds : bond 0.04566 ( 640) hydrogen bonds : angle 6.53100 ( 1680) link_BETA1-6 : bond 0.00089 ( 4) link_BETA1-6 : angle 1.68310 ( 12) SS BOND : bond 0.00382 ( 44) SS BOND : angle 0.75895 ( 88) covalent geometry : bond 0.00618 (20752) covalent geometry : angle 0.65581 (28168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8530 (mtpm) REVERT: C 46 GLU cc_start: 0.8112 (tt0) cc_final: 0.7745 (tt0) REVERT: C 63 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8227 (mtp-110) REVERT: I 17 GLU cc_start: 0.7894 (mp0) cc_final: 0.7550 (mp0) REVERT: I 24 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7707 (ttm110) REVERT: I 70 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7245 (mm-30) REVERT: I 79 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7618 (mp-120) REVERT: I 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8628 (pp20) REVERT: I 107 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.6970 (mm) REVERT: B 400 ARG cc_start: 0.8720 (ptm-80) cc_final: 0.8309 (ptm160) REVERT: F 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8525 (mtpm) REVERT: F 46 GLU cc_start: 0.8092 (tt0) cc_final: 0.7862 (tt0) REVERT: J 17 GLU cc_start: 0.7899 (mp0) cc_final: 0.7558 (mp0) REVERT: J 24 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7709 (ttm110) REVERT: J 70 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7224 (mm-30) REVERT: J 79 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7618 (mp-120) REVERT: J 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8627 (pp20) REVERT: J 107 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.6967 (mm) REVERT: A 400 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8301 (ptm160) REVERT: G 23 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8521 (mtpm) REVERT: G 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7814 (tt0) REVERT: K 17 GLU cc_start: 0.7884 (mp0) cc_final: 0.7536 (mp0) REVERT: K 24 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7611 (ttm110) REVERT: K 70 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7209 (mm-30) REVERT: K 79 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7607 (mp-120) REVERT: K 81 GLU cc_start: 0.8891 (pm20) cc_final: 0.8624 (pp20) REVERT: K 107 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.6964 (mm) REVERT: D 400 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8305 (ptm160) REVERT: H 23 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8535 (mtpm) REVERT: H 46 GLU cc_start: 0.8115 (tt0) cc_final: 0.7881 (tt0) REVERT: L 17 GLU cc_start: 0.7879 (mp0) cc_final: 0.7533 (mp0) REVERT: L 24 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7632 (ttm110) REVERT: L 70 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7267 (mm-30) REVERT: L 79 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7617 (mp-120) REVERT: L 81 GLU cc_start: 0.8897 (pm20) cc_final: 0.8630 (pp20) REVERT: L 107 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.6975 (mm) REVERT: E 400 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8298 (ptm160) outliers start: 28 outliers final: 20 residues processed: 213 average time/residue: 1.5009 time to fit residues: 357.8955 Evaluate side-chains 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 90 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 ASN B 468 HIS A 468 HIS D 441 ASN D 468 HIS E 441 ASN E 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054779 restraints weight = 37764.948| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.62 r_work: 0.2625 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20872 Z= 0.150 Angle : 0.618 6.940 28484 Z= 0.317 Chirality : 0.045 0.228 3292 Planarity : 0.004 0.045 3528 Dihedral : 7.379 59.867 4260 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.08 % Allowed : 11.10 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2488 helix: -0.88 (0.74), residues: 28 sheet: -0.29 (0.15), residues: 1088 loop : -0.03 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.003 0.001 HIS E 468 PHE 0.014 0.002 PHE D 410 TYR 0.011 0.001 TYR D 121 ARG 0.012 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 24) link_NAG-ASN : angle 2.34123 ( 72) link_ALPHA1-6 : bond 0.00508 ( 8) link_ALPHA1-6 : angle 1.36617 ( 24) link_BETA1-4 : bond 0.00370 ( 28) link_BETA1-4 : angle 1.70209 ( 84) link_ALPHA1-2 : bond 0.00630 ( 4) link_ALPHA1-2 : angle 2.29487 ( 12) link_ALPHA1-3 : bond 0.00928 ( 8) link_ALPHA1-3 : angle 1.69884 ( 24) hydrogen bonds : bond 0.03834 ( 640) hydrogen bonds : angle 6.22457 ( 1680) link_BETA1-6 : bond 0.00267 ( 4) link_BETA1-6 : angle 1.29064 ( 12) SS BOND : bond 0.00245 ( 44) SS BOND : angle 0.58037 ( 88) covalent geometry : bond 0.00335 (20752) covalent geometry : angle 0.59589 (28168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8448 (mtpm) REVERT: C 46 GLU cc_start: 0.8094 (tt0) cc_final: 0.7693 (tt0) REVERT: C 63 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8255 (mtp-110) REVERT: I 17 GLU cc_start: 0.7939 (mp0) cc_final: 0.7685 (mp0) REVERT: I 24 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7732 (ttm110) REVERT: I 54 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8293 (ttp80) REVERT: I 79 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7705 (mm-40) REVERT: I 81 GLU cc_start: 0.8893 (pm20) cc_final: 0.8639 (pp20) REVERT: I 107 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.6975 (mm) REVERT: B 400 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8283 (ptm160) REVERT: F 23 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8467 (mtpm) REVERT: F 46 GLU cc_start: 0.8105 (tt0) cc_final: 0.7884 (tt0) REVERT: J 17 GLU cc_start: 0.7941 (mp0) cc_final: 0.7690 (mp0) REVERT: J 24 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7728 (ttm110) REVERT: J 54 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8298 (ttp80) REVERT: J 79 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7732 (mm-40) REVERT: J 81 GLU cc_start: 0.8891 (pm20) cc_final: 0.8635 (pp20) REVERT: J 107 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7308 (pp) REVERT: A 400 ARG cc_start: 0.8680 (ptm-80) cc_final: 0.8274 (ptm160) REVERT: G 23 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8458 (mtpm) REVERT: G 46 GLU cc_start: 0.8165 (tt0) cc_final: 0.7704 (tt0) REVERT: K 17 GLU cc_start: 0.7944 (mp0) cc_final: 0.7692 (mp0) REVERT: K 24 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7715 (ttm110) REVERT: K 54 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8295 (ttp80) REVERT: K 79 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7726 (mm-40) REVERT: K 81 GLU cc_start: 0.8890 (pm20) cc_final: 0.8635 (pp20) REVERT: K 107 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7299 (pp) REVERT: D 400 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8279 (ptm160) REVERT: H 23 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8472 (mtpm) REVERT: H 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7871 (tt0) REVERT: L 17 GLU cc_start: 0.7955 (mp0) cc_final: 0.7612 (mp0) REVERT: L 24 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7750 (ttm110) REVERT: L 54 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8292 (ttp80) REVERT: L 79 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7731 (mm-40) REVERT: L 81 GLU cc_start: 0.8890 (pm20) cc_final: 0.8639 (pp20) REVERT: L 107 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7310 (pp) REVERT: E 400 ARG cc_start: 0.8683 (ptm-80) cc_final: 0.8270 (ptm160) outliers start: 23 outliers final: 16 residues processed: 215 average time/residue: 1.4535 time to fit residues: 350.0339 Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS G 65 GLN D 468 HIS E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053846 restraints weight = 38040.618| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.63 r_work: 0.2601 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20872 Z= 0.204 Angle : 0.648 6.902 28484 Z= 0.333 Chirality : 0.046 0.230 3292 Planarity : 0.004 0.051 3528 Dihedral : 7.369 59.765 4260 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.17 % Allowed : 11.99 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2488 helix: -0.01 (0.72), residues: 24 sheet: -0.28 (0.15), residues: 1080 loop : -0.04 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.003 0.001 HIS A 468 PHE 0.014 0.002 PHE A 410 TYR 0.014 0.002 TYR E 121 ARG 0.014 0.001 ARG K 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 24) link_NAG-ASN : angle 2.42778 ( 72) link_ALPHA1-6 : bond 0.00395 ( 8) link_ALPHA1-6 : angle 1.42292 ( 24) link_BETA1-4 : bond 0.00277 ( 28) link_BETA1-4 : angle 1.80238 ( 84) link_ALPHA1-2 : bond 0.00477 ( 4) link_ALPHA1-2 : angle 2.22108 ( 12) link_ALPHA1-3 : bond 0.00758 ( 8) link_ALPHA1-3 : angle 1.84203 ( 24) hydrogen bonds : bond 0.04093 ( 640) hydrogen bonds : angle 6.23915 ( 1680) link_BETA1-6 : bond 0.00132 ( 4) link_BETA1-6 : angle 1.41923 ( 12) SS BOND : bond 0.00329 ( 44) SS BOND : angle 0.63484 ( 88) covalent geometry : bond 0.00468 (20752) covalent geometry : angle 0.62534 (28168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8543 (mtpm) REVERT: C 46 GLU cc_start: 0.8126 (tt0) cc_final: 0.7746 (tt0) REVERT: C 63 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8287 (mtp-110) REVERT: I 17 GLU cc_start: 0.7967 (mp0) cc_final: 0.7707 (mp0) REVERT: I 24 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7678 (ttm110) REVERT: I 70 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7177 (mm-30) REVERT: I 79 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7623 (mp-120) REVERT: I 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8642 (pp20) REVERT: I 107 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7359 (pp) REVERT: B 400 ARG cc_start: 0.8727 (ptm-80) cc_final: 0.8350 (ptm160) REVERT: F 13 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8859 (mp0) REVERT: F 23 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8567 (mtpm) REVERT: F 46 GLU cc_start: 0.8123 (tt0) cc_final: 0.7910 (tt0) REVERT: J 17 GLU cc_start: 0.7957 (mp0) cc_final: 0.7699 (mp0) REVERT: J 24 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7694 (ttm110) REVERT: J 54 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8309 (ttp80) REVERT: J 70 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7214 (mm-30) REVERT: J 79 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7621 (mp-120) REVERT: J 81 GLU cc_start: 0.8895 (pm20) cc_final: 0.8639 (pp20) REVERT: J 107 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 400 ARG cc_start: 0.8716 (ptm-80) cc_final: 0.8340 (ptm160) REVERT: G 23 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8559 (mtpm) REVERT: G 46 GLU cc_start: 0.8192 (tt0) cc_final: 0.7728 (tt0) REVERT: K 17 GLU cc_start: 0.7961 (mp0) cc_final: 0.7702 (mp0) REVERT: K 24 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7661 (ttm110) REVERT: K 54 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8307 (ttp80) REVERT: K 70 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7212 (mm-30) REVERT: K 79 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7613 (mp-120) REVERT: K 81 GLU cc_start: 0.8890 (pm20) cc_final: 0.8637 (pp20) REVERT: K 107 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (pp) REVERT: D 400 ARG cc_start: 0.8720 (ptm-80) cc_final: 0.8345 (ptm160) REVERT: H 23 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8562 (mtpm) REVERT: H 46 GLU cc_start: 0.8111 (tt0) cc_final: 0.7901 (tt0) REVERT: L 17 GLU cc_start: 0.7958 (mp0) cc_final: 0.7685 (mp0) REVERT: L 24 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7686 (ttm110) REVERT: L 54 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8317 (ttp80) REVERT: L 70 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7199 (mm-30) REVERT: L 79 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7651 (mp-120) REVERT: L 81 GLU cc_start: 0.8898 (pm20) cc_final: 0.8643 (pp20) REVERT: L 107 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7362 (pp) REVERT: E 400 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8334 (ptm160) outliers start: 25 outliers final: 17 residues processed: 210 average time/residue: 1.4646 time to fit residues: 345.8109 Evaluate side-chains 214 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053463 restraints weight = 38080.823| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.63 r_work: 0.2592 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20872 Z= 0.223 Angle : 0.657 7.125 28484 Z= 0.337 Chirality : 0.046 0.235 3292 Planarity : 0.004 0.051 3528 Dihedral : 7.429 58.200 4260 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 1.45 % Allowed : 12.03 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2488 helix: -0.01 (0.74), residues: 24 sheet: -0.29 (0.15), residues: 1080 loop : -0.11 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 178 HIS 0.003 0.001 HIS E 468 PHE 0.015 0.002 PHE A 410 TYR 0.014 0.002 TYR E 121 ARG 0.014 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 24) link_NAG-ASN : angle 2.47327 ( 72) link_ALPHA1-6 : bond 0.00356 ( 8) link_ALPHA1-6 : angle 1.42889 ( 24) link_BETA1-4 : bond 0.00260 ( 28) link_BETA1-4 : angle 1.81181 ( 84) link_ALPHA1-2 : bond 0.00372 ( 4) link_ALPHA1-2 : angle 2.23050 ( 12) link_ALPHA1-3 : bond 0.00723 ( 8) link_ALPHA1-3 : angle 1.87361 ( 24) hydrogen bonds : bond 0.04197 ( 640) hydrogen bonds : angle 6.23917 ( 1680) link_BETA1-6 : bond 0.00043 ( 4) link_BETA1-6 : angle 1.50388 ( 12) SS BOND : bond 0.00321 ( 44) SS BOND : angle 0.63856 ( 88) covalent geometry : bond 0.00512 (20752) covalent geometry : angle 0.63416 (28168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8834 (mp0) REVERT: C 23 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8555 (mtpm) REVERT: C 63 ARG cc_start: 0.8654 (mtp-110) cc_final: 0.8301 (mtp-110) REVERT: I 17 GLU cc_start: 0.7972 (mp0) cc_final: 0.7718 (mp0) REVERT: I 24 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7634 (ttm110) REVERT: I 45 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8390 (mtp-110) REVERT: I 70 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7329 (mm-30) REVERT: I 79 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7480 (mp-120) REVERT: I 81 GLU cc_start: 0.8917 (pm20) cc_final: 0.8625 (pp20) REVERT: I 107 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7320 (pp) REVERT: B 400 ARG cc_start: 0.8742 (ptm-80) cc_final: 0.8343 (ptm160) REVERT: F 13 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8836 (mp0) REVERT: F 23 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8552 (mtpm) REVERT: J 17 GLU cc_start: 0.7971 (mp0) cc_final: 0.7718 (mp0) REVERT: J 24 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7696 (ttm110) REVERT: J 45 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8374 (mtp-110) REVERT: J 79 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7476 (mp-120) REVERT: J 81 GLU cc_start: 0.8911 (pm20) cc_final: 0.8618 (pp20) REVERT: J 107 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7327 (pp) REVERT: A 400 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8337 (ptm160) REVERT: G 13 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8838 (mp0) REVERT: G 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8547 (mtpm) REVERT: G 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7712 (tt0) REVERT: K 4 MET cc_start: 0.8608 (mmm) cc_final: 0.8009 (mmm) REVERT: K 17 GLU cc_start: 0.7975 (mp0) cc_final: 0.7722 (mp0) REVERT: K 24 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7501 (ttm110) REVERT: K 45 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8386 (mtp-110) REVERT: K 70 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7248 (mm-30) REVERT: K 79 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7476 (mp-120) REVERT: K 81 GLU cc_start: 0.8910 (pm20) cc_final: 0.8616 (pp20) REVERT: K 107 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7321 (pp) REVERT: D 400 ARG cc_start: 0.8741 (ptm-80) cc_final: 0.8342 (ptm160) REVERT: H 23 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8556 (mtpm) REVERT: H 46 GLU cc_start: 0.8118 (tt0) cc_final: 0.7910 (tt0) REVERT: L 17 GLU cc_start: 0.7983 (mp0) cc_final: 0.7729 (mp0) REVERT: L 24 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7649 (ttm110) REVERT: L 45 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8380 (mtp-110) REVERT: L 79 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7475 (mp-120) REVERT: L 81 GLU cc_start: 0.8914 (pm20) cc_final: 0.8616 (pp20) REVERT: L 107 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7322 (pp) REVERT: E 400 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8331 (ptm160) outliers start: 31 outliers final: 23 residues processed: 216 average time/residue: 1.5183 time to fit residues: 367.9532 Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 441 ASN A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.054466 restraints weight = 37763.095| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.61 r_work: 0.2617 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20872 Z= 0.165 Angle : 0.638 7.559 28484 Z= 0.327 Chirality : 0.045 0.237 3292 Planarity : 0.003 0.051 3528 Dihedral : 7.117 57.716 4260 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 12.13 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2488 helix: -0.88 (0.73), residues: 28 sheet: -0.24 (0.15), residues: 1080 loop : -0.10 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.004 0.001 HIS D 468 PHE 0.014 0.002 PHE D 410 TYR 0.012 0.001 TYR A 121 ARG 0.012 0.000 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 24) link_NAG-ASN : angle 2.32158 ( 72) link_ALPHA1-6 : bond 0.00466 ( 8) link_ALPHA1-6 : angle 1.40246 ( 24) link_BETA1-4 : bond 0.00324 ( 28) link_BETA1-4 : angle 1.67122 ( 84) link_ALPHA1-2 : bond 0.00509 ( 4) link_ALPHA1-2 : angle 2.25003 ( 12) link_ALPHA1-3 : bond 0.00893 ( 8) link_ALPHA1-3 : angle 1.76399 ( 24) hydrogen bonds : bond 0.03837 ( 640) hydrogen bonds : angle 6.08504 ( 1680) link_BETA1-6 : bond 0.00133 ( 4) link_BETA1-6 : angle 1.41149 ( 12) SS BOND : bond 0.00242 ( 44) SS BOND : angle 0.51166 ( 88) covalent geometry : bond 0.00377 (20752) covalent geometry : angle 0.61777 (28168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8829 (mp0) REVERT: C 23 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8494 (mtpm) REVERT: C 63 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8271 (mtp-110) REVERT: I 17 GLU cc_start: 0.7971 (mp0) cc_final: 0.7708 (mp0) REVERT: I 24 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7620 (ttm110) REVERT: I 45 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8380 (mtp-110) REVERT: I 54 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8328 (ttp80) REVERT: I 70 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7316 (mm-30) REVERT: I 79 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7660 (mm-40) REVERT: I 81 GLU cc_start: 0.8900 (pm20) cc_final: 0.8611 (pp20) REVERT: I 107 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7459 (pp) REVERT: B 400 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8326 (ptm160) REVERT: F 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8833 (mp0) REVERT: F 23 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8567 (mtpm) REVERT: J 17 GLU cc_start: 0.7961 (mp0) cc_final: 0.7700 (mp0) REVERT: J 24 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7639 (ttm110) REVERT: J 45 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8365 (mtp-110) REVERT: J 70 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7280 (mm-30) REVERT: J 79 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7652 (mm-40) REVERT: J 81 GLU cc_start: 0.8903 (pm20) cc_final: 0.8616 (pp20) REVERT: J 107 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7456 (pp) REVERT: A 400 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8319 (ptm160) REVERT: G 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8829 (mp0) REVERT: G 23 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8565 (mtpm) REVERT: G 46 GLU cc_start: 0.8149 (tt0) cc_final: 0.7662 (tt0) REVERT: K 17 GLU cc_start: 0.7965 (mp0) cc_final: 0.7703 (mp0) REVERT: K 24 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7616 (ttm110) REVERT: K 45 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8373 (mtp-110) REVERT: K 54 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8330 (ttp80) REVERT: K 70 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7319 (mm-30) REVERT: K 79 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7656 (mm-40) REVERT: K 81 GLU cc_start: 0.8902 (pm20) cc_final: 0.8613 (pp20) REVERT: K 107 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7453 (pp) REVERT: D 400 ARG cc_start: 0.8715 (ptm-80) cc_final: 0.8329 (ptm160) REVERT: H 13 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8820 (mp0) REVERT: H 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8565 (mtpm) REVERT: H 46 GLU cc_start: 0.8082 (tt0) cc_final: 0.7871 (tt0) REVERT: L 17 GLU cc_start: 0.7969 (mp0) cc_final: 0.7706 (mp0) REVERT: L 24 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7651 (ttm110) REVERT: L 45 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8365 (mtp-110) REVERT: L 54 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8324 (ttp80) REVERT: L 70 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7281 (mm-30) REVERT: L 79 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7655 (mm-40) REVERT: L 81 GLU cc_start: 0.8903 (pm20) cc_final: 0.8618 (pp20) REVERT: L 107 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7463 (pp) REVERT: E 400 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8314 (ptm160) outliers start: 34 outliers final: 25 residues processed: 224 average time/residue: 1.4159 time to fit residues: 356.5035 Evaluate side-chains 224 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 94 optimal weight: 2.9990 chunk 164 optimal weight: 0.0670 chunk 246 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053791 restraints weight = 37856.750| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.63 r_work: 0.2601 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20872 Z= 0.209 Angle : 0.652 7.609 28484 Z= 0.333 Chirality : 0.046 0.233 3292 Planarity : 0.004 0.050 3528 Dihedral : 7.194 57.203 4260 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 1.45 % Allowed : 12.55 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2488 helix: -0.01 (0.73), residues: 24 sheet: -0.27 (0.15), residues: 1080 loop : -0.14 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.004 0.001 HIS E 468 PHE 0.015 0.002 PHE D 410 TYR 0.013 0.002 TYR A 121 ARG 0.011 0.001 ARG K 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 24) link_NAG-ASN : angle 2.39614 ( 72) link_ALPHA1-6 : bond 0.00386 ( 8) link_ALPHA1-6 : angle 1.42424 ( 24) link_BETA1-4 : bond 0.00265 ( 28) link_BETA1-4 : angle 1.73684 ( 84) link_ALPHA1-2 : bond 0.00397 ( 4) link_ALPHA1-2 : angle 2.19439 ( 12) link_ALPHA1-3 : bond 0.00766 ( 8) link_ALPHA1-3 : angle 1.86427 ( 24) hydrogen bonds : bond 0.04050 ( 640) hydrogen bonds : angle 6.15158 ( 1680) link_BETA1-6 : bond 0.00065 ( 4) link_BETA1-6 : angle 1.46918 ( 12) SS BOND : bond 0.00305 ( 44) SS BOND : angle 0.64614 ( 88) covalent geometry : bond 0.00481 (20752) covalent geometry : angle 0.63078 (28168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8822 (mp0) REVERT: C 23 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8570 (mtpm) REVERT: I 17 GLU cc_start: 0.7990 (mp0) cc_final: 0.7728 (mp0) REVERT: I 24 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7603 (ttm110) REVERT: I 45 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8359 (mtp-110) REVERT: I 70 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7369 (mm-30) REVERT: I 81 GLU cc_start: 0.8901 (pm20) cc_final: 0.8663 (pp20) REVERT: I 107 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7492 (pp) REVERT: B 400 ARG cc_start: 0.8735 (ptm-80) cc_final: 0.8340 (ptm160) REVERT: F 13 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8827 (mp0) REVERT: F 23 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8577 (mtpm) REVERT: J 17 GLU cc_start: 0.7983 (mp0) cc_final: 0.7722 (mp0) REVERT: J 24 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7619 (ttm110) REVERT: J 45 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: J 47 LEU cc_start: 0.9001 (tp) cc_final: 0.8731 (tt) REVERT: J 70 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7359 (mm-30) REVERT: J 81 GLU cc_start: 0.8901 (pm20) cc_final: 0.8669 (pp20) REVERT: J 107 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7379 (pp) REVERT: A 400 ARG cc_start: 0.8726 (ptm-80) cc_final: 0.8336 (ptm160) REVERT: G 13 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8830 (mp0) REVERT: G 23 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8583 (mtpm) REVERT: G 46 GLU cc_start: 0.8164 (tt0) cc_final: 0.7671 (tt0) REVERT: K 17 GLU cc_start: 0.7985 (mp0) cc_final: 0.7724 (mp0) REVERT: K 24 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7613 (ttm110) REVERT: K 45 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: K 70 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7360 (mm-30) REVERT: K 81 GLU cc_start: 0.8901 (pm20) cc_final: 0.8663 (pp20) REVERT: K 107 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7486 (pp) REVERT: D 400 ARG cc_start: 0.8729 (ptm-80) cc_final: 0.8340 (ptm160) REVERT: H 13 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8818 (mp0) REVERT: H 23 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8568 (mtpm) REVERT: L 17 GLU cc_start: 0.7976 (mp0) cc_final: 0.7711 (mp0) REVERT: L 24 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7628 (ttm110) REVERT: L 45 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8350 (mtp-110) REVERT: L 54 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8345 (ttp80) REVERT: L 70 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7357 (mm-30) REVERT: L 81 GLU cc_start: 0.8903 (pm20) cc_final: 0.8669 (pp20) REVERT: L 107 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7493 (pp) REVERT: E 400 ARG cc_start: 0.8728 (ptm-80) cc_final: 0.8328 (ptm160) outliers start: 31 outliers final: 23 residues processed: 213 average time/residue: 1.3847 time to fit residues: 331.7039 Evaluate side-chains 214 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.055035 restraints weight = 37915.204| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.61 r_work: 0.2632 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20872 Z= 0.136 Angle : 0.621 7.402 28484 Z= 0.317 Chirality : 0.045 0.238 3292 Planarity : 0.003 0.047 3528 Dihedral : 6.900 57.403 4260 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 1.36 % Allowed : 12.55 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2488 helix: -0.92 (0.72), residues: 28 sheet: -0.23 (0.15), residues: 1080 loop : -0.08 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS E 468 PHE 0.014 0.001 PHE D 410 TYR 0.011 0.001 TYR D 121 ARG 0.011 0.000 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 24) link_NAG-ASN : angle 2.24479 ( 72) link_ALPHA1-6 : bond 0.00505 ( 8) link_ALPHA1-6 : angle 1.40894 ( 24) link_BETA1-4 : bond 0.00350 ( 28) link_BETA1-4 : angle 1.59557 ( 84) link_ALPHA1-2 : bond 0.00569 ( 4) link_ALPHA1-2 : angle 2.28281 ( 12) link_ALPHA1-3 : bond 0.00927 ( 8) link_ALPHA1-3 : angle 1.71754 ( 24) hydrogen bonds : bond 0.03672 ( 640) hydrogen bonds : angle 6.00730 ( 1680) link_BETA1-6 : bond 0.00183 ( 4) link_BETA1-6 : angle 1.37041 ( 12) SS BOND : bond 0.00204 ( 44) SS BOND : angle 0.50870 ( 88) covalent geometry : bond 0.00305 (20752) covalent geometry : angle 0.60104 (28168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15606.25 seconds wall clock time: 270 minutes 57.35 seconds (16257.35 seconds total)