Starting phenix.real_space_refine on Sun Aug 24 14:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3p_29707/08_2025/8g3p_29707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3p_29707/08_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_29707/08_2025/8g3p_29707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2025/8g3p_29707.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2025/8g3p_29707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2025/8g3p_29707.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.99, per 1000 atoms: 0.25 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: 1.60 Conformation dependent library (CDL) restraints added in 842.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.63 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: 3.88 Time building geometry restraints manager: 2.12 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 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: 0.010 Normalize map: mean=0, sd=1: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.710 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (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 ARG 0.019 0.003 ARG E 224 TYR 0.085 0.013 TYR B 281 PHE 0.060 0.013 PHE E 205 TRP 0.056 0.012 TRP J 97 HIS 0.021 0.006 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.01455 (20752) covalent geometry : angle 1.63736 (28168) SS BOND : bond 0.05062 ( 44) SS BOND : angle 2.33670 ( 88) hydrogen bonds : bond 0.15070 ( 640) hydrogen bonds : angle 8.49030 ( 1680) 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) 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_BETA1-6 : bond 0.01042 ( 4) link_BETA1-6 : angle 3.14322 ( 12) link_NAG-ASN : bond 0.01036 ( 24) link_NAG-ASN : angle 5.47149 ( 72) *********************** 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 : 0.780 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: 0.6875 time to fit residues: 221.2706 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 : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.085314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.055152 restraints weight = 37406.209| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.62 r_work: 0.2622 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20872 Z= 0.152 Angle : 0.710 8.679 28484 Z= 0.368 Chirality : 0.047 0.255 3292 Planarity : 0.004 0.042 3528 Dihedral : 9.023 75.480 4260 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 1.31 % Allowed : 7.35 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2488 helix: 0.23 (0.89), residues: 24 sheet: -0.04 (0.15), residues: 1068 loop : -0.29 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 45 TYR 0.014 0.002 TYR C 95 PHE 0.016 0.002 PHE D 410 TRP 0.023 0.002 TRP D 178 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00332 (20752) covalent geometry : angle 0.67978 (28168) SS BOND : bond 0.00351 ( 44) SS BOND : angle 0.59156 ( 88) hydrogen bonds : bond 0.04736 ( 640) hydrogen bonds : angle 7.15312 ( 1680) link_ALPHA1-2 : bond 0.00780 ( 4) link_ALPHA1-2 : angle 1.83075 ( 12) link_ALPHA1-3 : bond 0.01117 ( 8) link_ALPHA1-3 : angle 1.72641 ( 24) link_ALPHA1-6 : bond 0.00610 ( 8) link_ALPHA1-6 : angle 1.38573 ( 24) link_BETA1-4 : bond 0.00441 ( 28) link_BETA1-4 : angle 2.30639 ( 84) link_BETA1-6 : bond 0.00674 ( 4) link_BETA1-6 : angle 1.33763 ( 12) link_NAG-ASN : bond 0.00196 ( 24) link_NAG-ASN : angle 3.12869 ( 72) *********************** 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 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.516 Fit side-chains REVERT: C 23 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8550 (mtpm) REVERT: I 17 GLU cc_start: 0.7716 (mp0) cc_final: 0.7455 (mp0) REVERT: I 24 ARG cc_start: 0.7618 (ttm110) cc_final: 0.6808 (ttm110) REVERT: I 61 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.7400 (ptm-80) REVERT: I 79 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7563 (mp-120) REVERT: I 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8640 (pp20) REVERT: B 400 ARG cc_start: 0.8642 (ptm-80) cc_final: 0.8337 (ptm160) REVERT: F 23 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8537 (mtpm) REVERT: J 17 GLU cc_start: 0.7718 (mp0) cc_final: 0.7455 (mp0) REVERT: J 24 ARG cc_start: 0.7645 (ttm110) cc_final: 0.6824 (ttm110) REVERT: J 61 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: J 79 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7565 (mp-120) REVERT: J 81 GLU cc_start: 0.8908 (pm20) cc_final: 0.8643 (pp20) REVERT: A 400 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8345 (ptm160) REVERT: G 23 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8545 (mtpm) REVERT: K 17 GLU cc_start: 0.7711 (mp0) cc_final: 0.7449 (mp0) REVERT: K 24 ARG cc_start: 0.7615 (ttm110) cc_final: 0.6809 (ttm110) REVERT: K 61 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.7412 (ptm-80) REVERT: K 79 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7558 (mp-120) REVERT: K 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8642 (pp20) REVERT: D 400 ARG cc_start: 0.8646 (ptm-80) cc_final: 0.8347 (ptm160) REVERT: H 23 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8541 (mtpm) REVERT: L 17 GLU cc_start: 0.7711 (mp0) cc_final: 0.7450 (mp0) REVERT: L 24 ARG cc_start: 0.7609 (ttm110) cc_final: 0.6806 (ttm110) REVERT: L 61 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7404 (ptm-80) REVERT: L 79 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7558 (mp-120) REVERT: L 81 GLU cc_start: 0.8894 (pm20) cc_final: 0.8636 (pp20) REVERT: E 400 ARG cc_start: 0.8641 (ptm-80) cc_final: 0.8336 (ptm160) outliers start: 28 outliers final: 8 residues processed: 238 average time/residue: 0.7712 time to fit residues: 202.2479 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 0.0000 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3371 r_free = 0.3371 target = 0.085058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.055134 restraints weight = 37823.340| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.62 r_work: 0.2630 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2207 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= 0.151 Angle : 0.637 7.357 28484 Z= 0.333 Chirality : 0.046 0.242 3292 Planarity : 0.003 0.029 3528 Dihedral : 8.006 63.912 4260 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 1.97 % Allowed : 8.66 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2488 helix: 0.06 (0.78), residues: 24 sheet: -0.08 (0.15), residues: 1068 loop : -0.23 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 45 TYR 0.015 0.002 TYR D 121 PHE 0.014 0.002 PHE A 410 TRP 0.018 0.001 TRP E 178 HIS 0.003 0.001 HIS E 168 Details of bonding type rmsd covalent geometry : bond 0.00334 (20752) covalent geometry : angle 0.61232 (28168) SS BOND : bond 0.00253 ( 44) SS BOND : angle 0.46388 ( 88) hydrogen bonds : bond 0.04210 ( 640) hydrogen bonds : angle 6.68669 ( 1680) link_ALPHA1-2 : bond 0.00660 ( 4) link_ALPHA1-2 : angle 2.09546 ( 12) link_ALPHA1-3 : bond 0.00907 ( 8) link_ALPHA1-3 : angle 1.69420 ( 24) link_ALPHA1-6 : bond 0.00502 ( 8) link_ALPHA1-6 : angle 1.33617 ( 24) link_BETA1-4 : bond 0.00382 ( 28) link_BETA1-4 : angle 1.96921 ( 84) link_BETA1-6 : bond 0.00356 ( 4) link_BETA1-6 : angle 1.37950 ( 12) link_NAG-ASN : bond 0.00213 ( 24) link_NAG-ASN : angle 2.55358 ( 72) *********************** 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 263 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8456 (mtpm) REVERT: C 111 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: I 17 GLU cc_start: 0.7840 (mp0) cc_final: 0.7546 (mp0) REVERT: I 24 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7318 (ttm110) REVERT: I 61 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.7556 (ptm-80) REVERT: I 79 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7704 (mp-120) REVERT: I 81 GLU cc_start: 0.8908 (pm20) cc_final: 0.8616 (pp20) REVERT: I 107 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.6889 (mm) REVERT: B 400 ARG cc_start: 0.8643 (ptm-80) cc_final: 0.8315 (ptm160) REVERT: F 23 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8449 (mtpm) REVERT: F 63 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.8187 (mtp-110) REVERT: F 111 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: J 17 GLU cc_start: 0.7825 (mp0) cc_final: 0.7530 (mp0) REVERT: J 24 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7369 (ttm110) REVERT: J 61 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.7520 (ptm-80) REVERT: J 79 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7717 (mp-120) REVERT: J 81 GLU cc_start: 0.8911 (pm20) cc_final: 0.8618 (pp20) REVERT: J 107 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6866 (mm) REVERT: A 400 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8313 (ptm160) REVERT: G 23 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8443 (mtpm) REVERT: G 63 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8152 (mtp-110) REVERT: G 111 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: K 17 GLU cc_start: 0.7839 (mp0) cc_final: 0.7543 (mp0) REVERT: K 24 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7345 (ttm110) REVERT: K 61 ARG cc_start: 0.8486 (ptm-80) cc_final: 0.7529 (ptm-80) REVERT: K 79 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7700 (mp-120) REVERT: K 81 GLU cc_start: 0.8909 (pm20) cc_final: 0.8617 (pp20) REVERT: K 107 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.6860 (mm) REVERT: D 400 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8312 (ptm160) REVERT: H 23 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8455 (mtpm) REVERT: H 90 ASP cc_start: 0.7544 (m-30) cc_final: 0.7066 (m-30) REVERT: L 17 GLU cc_start: 0.7839 (mp0) cc_final: 0.7542 (mp0) REVERT: L 24 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7340 (ttm110) REVERT: L 61 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.7518 (ptm-80) REVERT: L 79 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7733 (mp-120) REVERT: L 81 GLU cc_start: 0.8913 (pm20) cc_final: 0.8620 (pp20) REVERT: L 107 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.6869 (mm) REVERT: E 400 ARG cc_start: 0.8637 (ptm-80) cc_final: 0.8307 (ptm160) outliers start: 42 outliers final: 20 residues processed: 237 average time/residue: 0.7419 time to fit residues: 193.2752 Evaluate side-chains 235 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 111 GLU 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 111 GLU 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 111 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS B 468 HIS F 65 GLN A 274 HIS A 468 HIS D 274 HIS D 468 HIS E 274 HIS E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053318 restraints weight = 37963.246| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.61 r_work: 0.2588 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20872 Z= 0.240 Angle : 0.664 7.449 28484 Z= 0.345 Chirality : 0.047 0.260 3292 Planarity : 0.004 0.038 3528 Dihedral : 8.018 62.965 4260 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 1.31 % Allowed : 9.93 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2488 helix: -0.07 (0.77), residues: 24 sheet: -0.20 (0.15), residues: 1088 loop : -0.21 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 45 TYR 0.016 0.002 TYR E 121 PHE 0.014 0.002 PHE D 410 TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00547 (20752) covalent geometry : angle 0.63809 (28168) SS BOND : bond 0.00346 ( 44) SS BOND : angle 0.59912 ( 88) hydrogen bonds : bond 0.04473 ( 640) hydrogen bonds : angle 6.66096 ( 1680) link_ALPHA1-2 : bond 0.00407 ( 4) link_ALPHA1-2 : angle 2.12295 ( 12) link_ALPHA1-3 : bond 0.00697 ( 8) link_ALPHA1-3 : angle 1.87980 ( 24) link_ALPHA1-6 : bond 0.00361 ( 8) link_ALPHA1-6 : angle 1.40299 ( 24) link_BETA1-4 : bond 0.00293 ( 28) link_BETA1-4 : angle 2.00719 ( 84) link_BETA1-6 : bond 0.00070 ( 4) link_BETA1-6 : angle 1.55959 ( 12) link_NAG-ASN : bond 0.00326 ( 24) link_NAG-ASN : angle 2.66199 ( 72) *********************** 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 237 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8458 (mtpm) REVERT: C 46 GLU cc_start: 0.8085 (tt0) cc_final: 0.7858 (tt0) REVERT: C 111 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: I 17 GLU cc_start: 0.7870 (mp0) cc_final: 0.7552 (mp0) REVERT: I 24 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7622 (ttm110) REVERT: I 70 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7092 (mm-30) REVERT: I 79 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7658 (mp-120) REVERT: I 81 GLU cc_start: 0.8906 (pm20) cc_final: 0.8623 (pp20) REVERT: I 107 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 400 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8302 (ptm160) REVERT: F 23 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8450 (mtpm) REVERT: F 46 GLU cc_start: 0.8078 (tt0) cc_final: 0.7800 (tt0) REVERT: F 65 GLN cc_start: 0.7969 (tp40) cc_final: 0.7733 (tp-100) REVERT: F 111 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: J 17 GLU cc_start: 0.7851 (mp0) cc_final: 0.7524 (mp0) REVERT: J 24 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7628 (ttm110) REVERT: J 70 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7092 (mm-30) REVERT: J 79 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7663 (mp-120) REVERT: J 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8620 (pp20) REVERT: J 107 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7016 (mm) REVERT: A 400 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8291 (ptm160) REVERT: G 23 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8448 (mtpm) REVERT: G 46 GLU cc_start: 0.8122 (tt0) cc_final: 0.7918 (tt0) REVERT: G 111 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: K 17 GLU cc_start: 0.7867 (mp0) cc_final: 0.7548 (mp0) REVERT: K 70 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7100 (mm-30) REVERT: K 79 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7649 (mp-120) REVERT: K 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8621 (pp20) REVERT: K 107 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7009 (mm) REVERT: D 400 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8293 (ptm160) REVERT: H 23 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8457 (mtpm) REVERT: H 46 GLU cc_start: 0.8099 (tt0) cc_final: 0.7723 (tt0) REVERT: H 63 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8148 (mtp-110) REVERT: H 65 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7789 (tp-100) REVERT: H 111 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: L 17 GLU cc_start: 0.7860 (mp0) cc_final: 0.7545 (mp0) REVERT: L 24 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7625 (ttm110) REVERT: L 70 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7095 (mm-30) REVERT: L 79 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7684 (mm-40) REVERT: L 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8617 (pp20) REVERT: L 107 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.6998 (mm) REVERT: E 400 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8288 (ptm160) outliers start: 28 outliers final: 21 residues processed: 225 average time/residue: 0.6885 time to fit residues: 171.6421 Evaluate side-chains 228 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 111 GLU 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 111 GLU 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 111 GLU 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 111 GLU 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 57 optimal weight: 2.9990 chunk 234 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 226 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN B 468 HIS F 32 GLN A 468 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS H 32 GLN E 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.053966 restraints weight = 37743.762| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.61 r_work: 0.2605 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2469 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= 0.186 Angle : 0.636 7.253 28484 Z= 0.329 Chirality : 0.046 0.238 3292 Planarity : 0.004 0.044 3528 Dihedral : 7.707 59.210 4260 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 1.50 % Allowed : 10.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.16), residues: 2488 helix: -0.03 (0.76), residues: 24 sheet: -0.25 (0.15), residues: 1088 loop : -0.14 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 45 TYR 0.013 0.001 TYR A 121 PHE 0.015 0.002 PHE B 410 TRP 0.018 0.001 TRP A 178 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00419 (20752) covalent geometry : angle 0.61186 (28168) SS BOND : bond 0.00295 ( 44) SS BOND : angle 0.65927 ( 88) hydrogen bonds : bond 0.04129 ( 640) hydrogen bonds : angle 6.43000 ( 1680) link_ALPHA1-2 : bond 0.00541 ( 4) link_ALPHA1-2 : angle 2.22164 ( 12) link_ALPHA1-3 : bond 0.00831 ( 8) link_ALPHA1-3 : angle 1.80378 ( 24) link_ALPHA1-6 : bond 0.00423 ( 8) link_ALPHA1-6 : angle 1.38442 ( 24) link_BETA1-4 : bond 0.00313 ( 28) link_BETA1-4 : angle 1.86249 ( 84) link_BETA1-6 : bond 0.00191 ( 4) link_BETA1-6 : angle 1.46002 ( 12) link_NAG-ASN : bond 0.00251 ( 24) link_NAG-ASN : angle 2.51133 ( 72) *********************** 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 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8475 (mtpm) REVERT: C 46 GLU cc_start: 0.8079 (tt0) cc_final: 0.7851 (tt0) REVERT: I 17 GLU cc_start: 0.7880 (mp0) cc_final: 0.7521 (mp0) REVERT: I 24 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7638 (ttm110) REVERT: I 70 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7229 (mm-30) REVERT: I 79 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7572 (mp-120) REVERT: I 81 GLU cc_start: 0.8911 (pm20) cc_final: 0.8628 (pp20) REVERT: I 107 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.6952 (mm) REVERT: B 400 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8304 (ptm160) REVERT: F 23 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8464 (mtpm) REVERT: F 46 GLU cc_start: 0.8074 (tt0) cc_final: 0.7804 (tt0) REVERT: J 4 MET cc_start: 0.8498 (mmm) cc_final: 0.8290 (mmm) REVERT: J 17 GLU cc_start: 0.7874 (mp0) cc_final: 0.7601 (mp0) REVERT: J 24 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7643 (ttm110) REVERT: J 70 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7200 (mm-30) REVERT: J 79 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7563 (mp-120) REVERT: J 81 GLU cc_start: 0.8915 (pm20) cc_final: 0.8638 (pp20) REVERT: J 107 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.6955 (mm) REVERT: A 400 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8289 (ptm160) REVERT: G 23 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8446 (mtpm) REVERT: G 46 GLU cc_start: 0.8102 (tt0) cc_final: 0.7889 (tt0) REVERT: K 17 GLU cc_start: 0.7893 (mp0) cc_final: 0.7538 (mp0) REVERT: K 79 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7565 (mp-120) REVERT: K 81 GLU cc_start: 0.8910 (pm20) cc_final: 0.8627 (pp20) REVERT: K 107 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.6951 (mm) REVERT: D 400 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8293 (ptm160) REVERT: H 23 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8472 (mtpm) REVERT: H 46 GLU cc_start: 0.8076 (tt0) cc_final: 0.7765 (tt0) REVERT: H 65 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7859 (tp-100) REVERT: L 4 MET cc_start: 0.8537 (mmm) cc_final: 0.8290 (mmm) REVERT: L 17 GLU cc_start: 0.7870 (mp0) cc_final: 0.7509 (mp0) REVERT: L 24 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7624 (ttm110) REVERT: L 70 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7233 (mm-30) REVERT: L 79 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7571 (mp-120) REVERT: L 81 GLU cc_start: 0.8916 (pm20) cc_final: 0.8634 (pp20) REVERT: L 107 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.6961 (mm) REVERT: E 400 ARG cc_start: 0.8687 (ptm-80) cc_final: 0.8284 (ptm160) outliers start: 32 outliers final: 21 residues processed: 216 average time/residue: 0.6776 time to fit residues: 162.9311 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 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 243 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 441 ASN A 468 HIS D 441 ASN D 468 HIS E 441 ASN E 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054565 restraints weight = 37754.257| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.61 r_work: 0.2621 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20872 Z= 0.157 Angle : 0.622 6.947 28484 Z= 0.320 Chirality : 0.045 0.242 3292 Planarity : 0.004 0.048 3528 Dihedral : 7.370 55.404 4260 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.31 % Allowed : 11.19 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2488 helix: -0.82 (0.75), residues: 28 sheet: -0.26 (0.15), residues: 1088 loop : -0.08 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 45 TYR 0.012 0.001 TYR A 121 PHE 0.014 0.002 PHE D 410 TRP 0.016 0.001 TRP D 178 HIS 0.003 0.001 HIS E 468 Details of bonding type rmsd covalent geometry : bond 0.00352 (20752) covalent geometry : angle 0.59896 (28168) SS BOND : bond 0.00230 ( 44) SS BOND : angle 0.57780 ( 88) hydrogen bonds : bond 0.03892 ( 640) hydrogen bonds : angle 6.26207 ( 1680) link_ALPHA1-2 : bond 0.00598 ( 4) link_ALPHA1-2 : angle 2.23567 ( 12) link_ALPHA1-3 : bond 0.00917 ( 8) link_ALPHA1-3 : angle 1.79321 ( 24) link_ALPHA1-6 : bond 0.00471 ( 8) link_ALPHA1-6 : angle 1.38348 ( 24) link_BETA1-4 : bond 0.00331 ( 28) link_BETA1-4 : angle 1.76090 ( 84) link_BETA1-6 : bond 0.00263 ( 4) link_BETA1-6 : angle 1.31200 ( 12) link_NAG-ASN : bond 0.00207 ( 24) link_NAG-ASN : angle 2.39885 ( 72) *********************** 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 226 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8588 (mtpm) REVERT: C 46 GLU cc_start: 0.8053 (tt0) cc_final: 0.7826 (tt0) REVERT: I 17 GLU cc_start: 0.7926 (mp0) cc_final: 0.7671 (mp0) REVERT: I 24 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7671 (ttm110) REVERT: I 70 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7199 (mm-30) REVERT: I 79 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7529 (mp-120) REVERT: I 81 GLU cc_start: 0.8908 (pm20) cc_final: 0.8645 (pp20) REVERT: I 107 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 400 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8285 (ptm160) REVERT: F 23 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8583 (mtpm) REVERT: F 46 GLU cc_start: 0.8108 (tt0) cc_final: 0.7855 (tt0) REVERT: J 17 GLU cc_start: 0.7912 (mp0) cc_final: 0.7661 (mp0) REVERT: J 24 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7611 (ttm110) REVERT: J 70 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7224 (mm-30) REVERT: J 79 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7537 (mp-120) REVERT: J 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8643 (pp20) REVERT: J 107 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.6957 (mm) REVERT: A 400 ARG cc_start: 0.8685 (ptm-80) cc_final: 0.8316 (ptm160) REVERT: G 23 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8437 (mtpm) REVERT: K 17 GLU cc_start: 0.7905 (mp0) cc_final: 0.7657 (mp0) REVERT: K 79 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7522 (mp-120) REVERT: K 81 GLU cc_start: 0.8905 (pm20) cc_final: 0.8642 (pp20) REVERT: K 107 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.6948 (mm) REVERT: D 400 ARG cc_start: 0.8690 (ptm-80) cc_final: 0.8319 (ptm160) REVERT: H 23 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8541 (mtpm) REVERT: H 46 GLU cc_start: 0.8083 (tt0) cc_final: 0.7827 (tt0) REVERT: H 65 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7936 (tp-100) REVERT: L 17 GLU cc_start: 0.7916 (mp0) cc_final: 0.7660 (mp0) REVERT: L 24 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7599 (ttm110) REVERT: L 70 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7214 (mm-30) REVERT: L 79 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7597 (mp-120) REVERT: L 81 GLU cc_start: 0.8910 (pm20) cc_final: 0.8647 (pp20) REVERT: L 107 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7304 (pp) REVERT: E 400 ARG cc_start: 0.8681 (ptm-80) cc_final: 0.8310 (ptm160) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.6497 time to fit residues: 158.3092 Evaluate side-chains 222 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 164 optimal weight: 0.0980 chunk 244 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN B 468 HIS A 468 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3383 r_free = 0.3383 target = 0.085450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055725 restraints weight = 37983.602| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.63 r_work: 0.2647 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20872 Z= 0.127 Angle : 0.603 6.723 28484 Z= 0.308 Chirality : 0.045 0.239 3292 Planarity : 0.003 0.047 3528 Dihedral : 6.871 56.553 4260 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 1.31 % Allowed : 11.42 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2488 helix: -0.79 (0.74), residues: 28 sheet: -0.23 (0.15), residues: 1088 loop : 0.01 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 45 TYR 0.011 0.001 TYR A 121 PHE 0.013 0.001 PHE E 410 TRP 0.016 0.001 TRP D 178 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00281 (20752) covalent geometry : angle 0.58333 (28168) SS BOND : bond 0.00331 ( 44) SS BOND : angle 0.43923 ( 88) hydrogen bonds : bond 0.03592 ( 640) hydrogen bonds : angle 6.03579 ( 1680) link_ALPHA1-2 : bond 0.00677 ( 4) link_ALPHA1-2 : angle 2.24927 ( 12) link_ALPHA1-3 : bond 0.00938 ( 8) link_ALPHA1-3 : angle 1.67075 ( 24) link_ALPHA1-6 : bond 0.00571 ( 8) link_ALPHA1-6 : angle 1.37509 ( 24) link_BETA1-4 : bond 0.00376 ( 28) link_BETA1-4 : angle 1.61988 ( 84) link_BETA1-6 : bond 0.00307 ( 4) link_BETA1-6 : angle 1.26327 ( 12) link_NAG-ASN : bond 0.00155 ( 24) link_NAG-ASN : angle 2.18979 ( 72) *********************** 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 233 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8852 (mp0) REVERT: C 46 GLU cc_start: 0.8045 (tt0) cc_final: 0.7817 (tt0) REVERT: I 4 MET cc_start: 0.8503 (mmm) cc_final: 0.7954 (mmm) REVERT: I 17 GLU cc_start: 0.7946 (mp0) cc_final: 0.7687 (mp0) REVERT: I 24 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7544 (ttm110) REVERT: I 45 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8281 (mtp-110) REVERT: I 54 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8318 (ttp80) REVERT: I 70 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7325 (mm-30) REVERT: I 79 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7629 (mp-120) REVERT: I 81 GLU cc_start: 0.8895 (pm20) cc_final: 0.8638 (pp20) REVERT: I 107 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (pp) REVERT: B 400 ARG cc_start: 0.8684 (ptm-80) cc_final: 0.8307 (ptm160) REVERT: F 13 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8853 (mp0) REVERT: F 46 GLU cc_start: 0.8141 (tt0) cc_final: 0.7878 (tt0) REVERT: J 17 GLU cc_start: 0.7945 (mp0) cc_final: 0.7680 (mp0) REVERT: J 24 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7661 (ttm110) REVERT: J 45 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8284 (mtp-110) REVERT: J 54 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8291 (ttp80) REVERT: J 70 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7319 (mm-30) REVERT: J 79 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7632 (mp-120) REVERT: J 81 GLU cc_start: 0.8893 (pm20) cc_final: 0.8635 (pp20) REVERT: J 107 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7321 (pp) REVERT: A 400 ARG cc_start: 0.8676 (ptm-80) cc_final: 0.8299 (ptm160) REVERT: G 13 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8859 (mp0) REVERT: G 23 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8458 (mtpm) REVERT: K 4 MET cc_start: 0.8471 (mmm) cc_final: 0.8005 (mmm) REVERT: K 17 GLU cc_start: 0.7940 (mp0) cc_final: 0.7683 (mp0) REVERT: K 24 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7471 (ttm110) REVERT: K 45 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8288 (mtp-110) REVERT: K 54 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8310 (ttp80) REVERT: K 79 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7621 (mp-120) REVERT: K 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8642 (pp20) REVERT: K 107 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7327 (pp) REVERT: D 400 ARG cc_start: 0.8680 (ptm-80) cc_final: 0.8301 (ptm160) REVERT: H 46 GLU cc_start: 0.8131 (tt0) cc_final: 0.7857 (tt0) REVERT: H 65 GLN cc_start: 0.8349 (tp-100) cc_final: 0.8007 (tp-100) REVERT: L 4 MET cc_start: 0.8511 (mmm) cc_final: 0.8125 (mmm) REVERT: L 17 GLU cc_start: 0.7947 (mp0) cc_final: 0.7669 (mp0) REVERT: L 24 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7550 (ttm110) REVERT: L 45 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.8274 (mtp-110) REVERT: L 54 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8295 (ttp80) REVERT: L 70 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7316 (mm-30) REVERT: L 79 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7628 (mp-120) REVERT: L 81 GLU cc_start: 0.8884 (pm20) cc_final: 0.8638 (pp20) REVERT: L 107 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7315 (pp) REVERT: E 400 ARG cc_start: 0.8666 (ptm-80) cc_final: 0.8289 (ptm160) outliers start: 28 outliers final: 18 residues processed: 221 average time/residue: 0.6597 time to fit residues: 162.7520 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 105 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.084959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.055220 restraints weight = 37879.690| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.64 r_work: 0.2637 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20872 Z= 0.154 Angle : 0.616 6.865 28484 Z= 0.314 Chirality : 0.045 0.237 3292 Planarity : 0.003 0.043 3528 Dihedral : 6.839 57.646 4260 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 1.17 % Allowed : 12.64 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.16), residues: 2488 helix: -0.71 (0.76), residues: 28 sheet: -0.24 (0.15), residues: 1056 loop : -0.05 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 45 TYR 0.012 0.001 TYR B 121 PHE 0.013 0.002 PHE A 410 TRP 0.014 0.001 TRP E 178 HIS 0.004 0.001 HIS E 468 Details of bonding type rmsd covalent geometry : bond 0.00351 (20752) covalent geometry : angle 0.59605 (28168) SS BOND : bond 0.00250 ( 44) SS BOND : angle 0.54742 ( 88) hydrogen bonds : bond 0.03705 ( 640) hydrogen bonds : angle 6.03663 ( 1680) link_ALPHA1-2 : bond 0.00587 ( 4) link_ALPHA1-2 : angle 2.18009 ( 12) link_ALPHA1-3 : bond 0.00878 ( 8) link_ALPHA1-3 : angle 1.73093 ( 24) link_ALPHA1-6 : bond 0.00522 ( 8) link_ALPHA1-6 : angle 1.39630 ( 24) link_BETA1-4 : bond 0.00331 ( 28) link_BETA1-4 : angle 1.64450 ( 84) link_BETA1-6 : bond 0.00246 ( 4) link_BETA1-6 : angle 1.31159 ( 12) link_NAG-ASN : bond 0.00193 ( 24) link_NAG-ASN : angle 2.22608 ( 72) *********************** 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 228 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.659 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: C 13 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8840 (mp0) REVERT: C 46 GLU cc_start: 0.8033 (tt0) cc_final: 0.7704 (tt0) REVERT: I 17 GLU cc_start: 0.7953 (mp0) cc_final: 0.7695 (mp0) REVERT: I 24 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7617 (ttm110) REVERT: I 70 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7335 (mm-30) REVERT: I 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8660 (pp20) REVERT: I 107 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7351 (pp) REVERT: B 400 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8334 (ptm160) REVERT: F 13 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8842 (mp0) REVERT: F 46 GLU cc_start: 0.8140 (tt0) cc_final: 0.7877 (tt0) REVERT: J 17 GLU cc_start: 0.7956 (mp0) cc_final: 0.7688 (mp0) REVERT: J 24 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7623 (ttm110) REVERT: J 70 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7326 (mm-30) REVERT: J 79 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7607 (mp-120) REVERT: J 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8647 (pp20) REVERT: J 107 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7362 (pp) REVERT: A 400 ARG cc_start: 0.8687 (ptm-80) cc_final: 0.8336 (ptm160) REVERT: G 13 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8859 (mp0) REVERT: K 17 GLU cc_start: 0.7955 (mp0) cc_final: 0.7696 (mp0) REVERT: K 54 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8332 (ttp80) REVERT: K 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8657 (pp20) REVERT: K 107 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7351 (pp) REVERT: D 400 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8342 (ptm160) REVERT: H 46 GLU cc_start: 0.8135 (tt0) cc_final: 0.7861 (tt0) REVERT: H 65 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8008 (tp-100) REVERT: L 17 GLU cc_start: 0.7958 (mp0) cc_final: 0.7704 (mp0) REVERT: L 24 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7621 (ttm110) REVERT: L 70 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7323 (mm-30) REVERT: L 81 GLU cc_start: 0.8894 (pm20) cc_final: 0.8659 (pp20) REVERT: L 107 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7356 (pp) REVERT: E 400 ARG cc_start: 0.8676 (ptm-80) cc_final: 0.8323 (ptm160) outliers start: 25 outliers final: 16 residues processed: 219 average time/residue: 0.6404 time to fit residues: 157.0214 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 : 0.603 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.084262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.054472 restraints weight = 37797.130| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.62 r_work: 0.2618 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20872 Z= 0.181 Angle : 0.639 7.084 28484 Z= 0.327 Chirality : 0.045 0.240 3292 Planarity : 0.004 0.056 3528 Dihedral : 6.952 59.926 4260 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 1.22 % Allowed : 12.64 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2488 helix: -0.72 (0.77), residues: 28 sheet: -0.18 (0.15), residues: 1040 loop : -0.08 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 45 TYR 0.013 0.001 TYR D 121 PHE 0.015 0.002 PHE E 410 TRP 0.015 0.001 TRP E 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00413 (20752) covalent geometry : angle 0.61803 (28168) SS BOND : bond 0.00300 ( 44) SS BOND : angle 0.59278 ( 88) hydrogen bonds : bond 0.03911 ( 640) hydrogen bonds : angle 6.06605 ( 1680) link_ALPHA1-2 : bond 0.00483 ( 4) link_ALPHA1-2 : angle 2.15905 ( 12) link_ALPHA1-3 : bond 0.00807 ( 8) link_ALPHA1-3 : angle 1.81730 ( 24) link_ALPHA1-6 : bond 0.00440 ( 8) link_ALPHA1-6 : angle 1.42180 ( 24) link_BETA1-4 : bond 0.00286 ( 28) link_BETA1-4 : angle 1.69066 ( 84) link_BETA1-6 : bond 0.00145 ( 4) link_BETA1-6 : angle 1.40657 ( 12) link_NAG-ASN : bond 0.00254 ( 24) link_NAG-ASN : angle 2.31927 ( 72) *********************** 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 228 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8851 (mp0) REVERT: C 46 GLU cc_start: 0.8088 (tt0) cc_final: 0.7759 (tt0) REVERT: I 17 GLU cc_start: 0.7982 (mp0) cc_final: 0.7724 (mp0) REVERT: I 24 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7528 (ttm110) REVERT: I 70 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7330 (mm-30) REVERT: I 79 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7727 (mm-40) REVERT: I 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8634 (pp20) REVERT: I 107 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (pp) REVERT: B 400 ARG cc_start: 0.8705 (ptm-80) cc_final: 0.8328 (ptm160) REVERT: F 13 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8853 (mp0) REVERT: F 46 GLU cc_start: 0.8173 (tt0) cc_final: 0.7892 (tt0) REVERT: J 24 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7599 (ttm110) REVERT: J 70 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7405 (mm-30) REVERT: J 79 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7681 (mm-40) REVERT: J 81 GLU cc_start: 0.8906 (pm20) cc_final: 0.8634 (pp20) REVERT: J 107 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7397 (pp) REVERT: A 400 ARG cc_start: 0.8705 (ptm-80) cc_final: 0.8330 (ptm160) REVERT: G 13 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8870 (mp0) REVERT: G 23 LYS cc_start: 0.8567 (mtpm) cc_final: 0.8249 (mtpm) REVERT: K 17 GLU cc_start: 0.7985 (mp0) cc_final: 0.7727 (mp0) REVERT: K 79 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7725 (mm-40) REVERT: K 81 GLU cc_start: 0.8903 (pm20) cc_final: 0.8632 (pp20) REVERT: K 107 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7389 (pp) REVERT: D 400 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8333 (ptm160) REVERT: H 13 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8853 (mp0) REVERT: H 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7883 (tt0) REVERT: H 65 GLN cc_start: 0.8406 (tp-100) cc_final: 0.7993 (tp-100) REVERT: L 17 GLU cc_start: 0.7970 (mp0) cc_final: 0.7708 (mp0) REVERT: L 24 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7528 (ttm110) REVERT: L 70 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7316 (mm-30) REVERT: L 79 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7717 (mm-40) REVERT: L 81 GLU cc_start: 0.8909 (pm20) cc_final: 0.8659 (pp20) REVERT: L 107 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7411 (pp) REVERT: E 400 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8320 (ptm160) outliers start: 26 outliers final: 17 residues processed: 219 average time/residue: 0.6891 time to fit residues: 167.6660 Evaluate side-chains 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 19 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.054467 restraints weight = 37853.172| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.62 r_work: 0.2619 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 20872 Z= 0.201 Angle : 0.790 61.598 28484 Z= 0.386 Chirality : 0.046 0.457 3292 Planarity : 0.004 0.055 3528 Dihedral : 6.958 59.960 4260 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 0.98 % Allowed : 13.30 % Favored : 85.72 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2488 helix: -0.73 (0.77), residues: 28 sheet: -0.17 (0.15), residues: 1040 loop : -0.09 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 18 TYR 0.013 0.001 TYR D 121 PHE 0.015 0.002 PHE E 410 TRP 0.015 0.001 TRP E 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00456 (20752) covalent geometry : angle 0.77458 (28168) SS BOND : bond 0.00336 ( 44) SS BOND : angle 0.73064 ( 88) hydrogen bonds : bond 0.03922 ( 640) hydrogen bonds : angle 6.06643 ( 1680) link_ALPHA1-2 : bond 0.00465 ( 4) link_ALPHA1-2 : angle 2.16816 ( 12) link_ALPHA1-3 : bond 0.00784 ( 8) link_ALPHA1-3 : angle 1.80567 ( 24) link_ALPHA1-6 : bond 0.00442 ( 8) link_ALPHA1-6 : angle 1.42536 ( 24) link_BETA1-4 : bond 0.00272 ( 28) link_BETA1-4 : angle 1.70014 ( 84) link_BETA1-6 : bond 0.00144 ( 4) link_BETA1-6 : angle 1.41050 ( 12) link_NAG-ASN : bond 0.00253 ( 24) link_NAG-ASN : angle 2.31777 ( 72) ********************** 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 216 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8851 (mp0) REVERT: C 46 GLU cc_start: 0.8085 (tt0) cc_final: 0.7755 (tt0) REVERT: I 17 GLU cc_start: 0.7988 (mp0) cc_final: 0.7723 (mp0) REVERT: I 24 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7527 (ttm110) REVERT: I 70 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7332 (mm-30) REVERT: I 79 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7727 (mm-40) REVERT: I 81 GLU cc_start: 0.8910 (pm20) cc_final: 0.8633 (pp20) REVERT: I 107 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7408 (pp) REVERT: B 400 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8333 (ptm160) REVERT: F 13 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8853 (mp0) REVERT: F 46 GLU cc_start: 0.8168 (tt0) cc_final: 0.7886 (tt0) REVERT: F 90 ASP cc_start: 0.7595 (m-30) cc_final: 0.7165 (m-30) REVERT: J 24 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7594 (ttm110) REVERT: J 70 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7405 (mm-30) REVERT: J 79 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7710 (mm110) REVERT: J 81 GLU cc_start: 0.8910 (pm20) cc_final: 0.8630 (pp20) REVERT: J 107 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7394 (pp) REVERT: A 400 ARG cc_start: 0.8708 (ptm-80) cc_final: 0.8334 (ptm160) REVERT: G 13 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8866 (mp0) REVERT: G 23 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8246 (mtpm) REVERT: K 17 GLU cc_start: 0.7985 (mp0) cc_final: 0.7721 (mp0) REVERT: K 79 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7725 (mm-40) REVERT: K 81 GLU cc_start: 0.8907 (pm20) cc_final: 0.8630 (pp20) REVERT: K 107 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7385 (pp) REVERT: D 400 ARG cc_start: 0.8713 (ptm-80) cc_final: 0.8338 (ptm160) REVERT: H 13 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8852 (mp0) REVERT: H 46 GLU cc_start: 0.8172 (tt0) cc_final: 0.7877 (tt0) REVERT: H 65 GLN cc_start: 0.8406 (tp-100) cc_final: 0.7990 (tp-100) REVERT: L 17 GLU cc_start: 0.7970 (mp0) cc_final: 0.7706 (mp0) REVERT: L 24 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7511 (ttm110) REVERT: L 70 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7296 (mm-30) REVERT: L 79 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7714 (mm-40) REVERT: L 81 GLU cc_start: 0.8915 (pm20) cc_final: 0.8657 (pp20) REVERT: L 107 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7408 (pp) REVERT: E 400 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8324 (ptm160) outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 0.6856 time to fit residues: 157.9700 Evaluate side-chains 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.084978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055265 restraints weight = 37774.747| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.62 r_work: 0.2638 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 20872 Z= 0.154 Angle : 0.652 12.227 28484 Z= 0.333 Chirality : 0.045 0.241 3292 Planarity : 0.004 0.083 3528 Dihedral : 6.753 56.066 4260 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.31 % Allowed : 12.87 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.17), residues: 2488 helix: -0.71 (0.77), residues: 28 sheet: -0.23 (0.15), residues: 1056 loop : -0.05 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 18 TYR 0.011 0.001 TYR B 121 PHE 0.014 0.002 PHE A 410 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00344 (20752) covalent geometry : angle 0.63449 (28168) SS BOND : bond 0.00232 ( 44) SS BOND : angle 0.53645 ( 88) hydrogen bonds : bond 0.03687 ( 640) hydrogen bonds : angle 5.98104 ( 1680) link_ALPHA1-2 : bond 0.00586 ( 4) link_ALPHA1-2 : angle 2.17513 ( 12) link_ALPHA1-3 : bond 0.00918 ( 8) link_ALPHA1-3 : angle 1.74814 ( 24) link_ALPHA1-6 : bond 0.00509 ( 8) link_ALPHA1-6 : angle 1.39734 ( 24) link_BETA1-4 : bond 0.00367 ( 28) link_BETA1-4 : angle 1.58122 ( 84) link_BETA1-6 : bond 0.00199 ( 4) link_BETA1-6 : angle 1.33695 ( 12) link_NAG-ASN : bond 0.00181 ( 24) link_NAG-ASN : angle 2.20903 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7673.78 seconds wall clock time: 131 minutes 27.68 seconds (7887.68 seconds total)