Starting phenix.real_space_refine on Sun Aug 24 14:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3n_29705/08_2025/8g3n_29705.cif" } resolution = 2.9 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= 0.001 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 12564 2.51 5 N 3434 2.21 5 O 4202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 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: 39 Chain: "G" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" 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: "F" 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: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" 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: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" 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: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "t" Number of atoms: 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "V" 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "Z" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "X" 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: "a" 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: "G" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "L" 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: 5.12, per 1000 atoms: 0.25 Number of scatterers: 20321 At special positions: 0 Unit cell: (149.741, 149.741, 106.021, 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 4202 8.00 N 3434 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.05 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.10 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.10 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.13 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.09 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.09 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.15 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.09 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.22 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.07 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.08 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.10 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.10 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.13 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.09 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.09 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.15 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.22 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.07 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.08 Simple disulfide: pdb=" SG CYS K 92 " - pdb=" SG CYS K 417 " distance=2.05 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 129 " distance=2.10 Simple disulfide: pdb=" SG CYS K 175 " - pdb=" SG CYS K 193 " distance=2.10 Simple disulfide: pdb=" SG CYS K 183 " - pdb=" SG CYS K 230 " distance=2.13 Simple disulfide: pdb=" SG CYS K 232 " - pdb=" SG CYS K 237 " distance=2.09 Simple disulfide: pdb=" SG CYS K 278 " - pdb=" SG CYS K 291 " distance=2.09 Simple disulfide: pdb=" SG CYS K 280 " - pdb=" SG CYS K 289 " distance=2.15 Simple disulfide: pdb=" SG CYS K 318 " - pdb=" SG CYS K 337 " distance=2.09 Simple disulfide: pdb=" SG CYS K 421 " - pdb=" SG CYS K 447 " distance=2.22 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.08 Simple disulfide: pdb=" SG CYS L 92 " - pdb=" SG CYS L 417 " distance=2.05 Simple disulfide: pdb=" SG CYS L 124 " - pdb=" SG CYS L 129 " distance=2.10 Simple disulfide: pdb=" SG CYS L 175 " - pdb=" SG CYS L 193 " distance=2.10 Simple disulfide: pdb=" SG CYS L 183 " - pdb=" SG CYS L 230 " distance=2.13 Simple disulfide: pdb=" SG CYS L 232 " - pdb=" SG CYS L 237 " distance=2.09 Simple disulfide: pdb=" SG CYS L 278 " - pdb=" SG CYS L 291 " distance=2.09 Simple disulfide: pdb=" SG CYS L 280 " - pdb=" SG CYS L 289 " distance=2.15 Simple disulfide: pdb=" SG CYS L 318 " - pdb=" SG CYS L 337 " distance=2.09 Simple disulfide: pdb=" SG CYS L 421 " - pdb=" SG CYS L 447 " distance=2.22 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.07 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.08 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG 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 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 r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG V 1 " - " FUC V 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG M 1 " - " ASN J 86 " " NAG N 1 " - " ASN K 86 " " NAG O 1 " - " ASN L 86 " " NAG P 1 " - " ASN J 146 " " NAG Q 1 " - " ASN K 146 " " NAG R 1 " - " ASN L 146 " " NAG S 1 " - " ASN J 200 " " NAG T 1 " - " ASN K 200 " " NAG U 1 " - " ASN L 200 " " NAG V 1 " - " ASN J 234 " " NAG W 1 " - " ASN K 234 " " NAG X 1 " - " ASN L 234 " " NAG Z 1 " - " ASN K 329 " " NAG a 1 " - " ASN L 329 " " NAG b 1 " - " ASN J 367 " " NAG c 1 " - " ASN K 367 " " NAG d 1 " - " ASN L 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 704.2 milliseconds Enol-peptide restraints added in 715.3 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: 4552 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 44 sheets defined 4.1% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.595A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.688A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 removed outlier: 3.614A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.596A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.690A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.595A pdb=" N ASN K 146 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.689A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.595A pdb=" N ASN L 146 " --> pdb=" O VAL L 143 " (cutoff:3.500A) 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: 3.689A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.621A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.860A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 3.620A pdb=" N SER G 179 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.734A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.435A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.841A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY G 363 " --> pdb=" O TRP G 352 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.792A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.886A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.487A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU F 13 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.622A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.860A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 179 through 184 removed outlier: 3.620A pdb=" N SER J 179 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.736A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.436A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.842A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY J 363 " --> pdb=" O TRP J 352 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.484A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.458A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.458A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 117 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU D 13 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 96 through 102 removed outlier: 3.621A pdb=" N GLY K 96 " --> pdb=" O THR K 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL K 445 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS K 102 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE K 443 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG K 420 " --> pdb=" O GLY K 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 115 through 124 removed outlier: 4.861A pdb=" N TRP K 115 " --> pdb=" O THR K 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR K 138 " --> pdb=" O TRP K 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR K 157 " --> pdb=" O GLY K 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 158 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS K 172 " --> pdb=" O MET K 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 179 through 184 removed outlier: 3.620A pdb=" N SER K 179 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP K 197 " --> pdb=" O ASN K 200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 213 " --> pdb=" O PHE K 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR K 207 " --> pdb=" O LEU K 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU K 211 " --> pdb=" O TYR K 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 231 through 233 removed outlier: 3.735A pdb=" N VAL K 231 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU K 258 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE K 262 " --> pdb=" O GLU K 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 276 through 283 removed outlier: 5.435A pdb=" N GLU K 277 " --> pdb=" O ARG K 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG K 292 " --> pdb=" O GLU K 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 352 through 356 removed outlier: 4.841A pdb=" N TRP K 352 " --> pdb=" O GLY K 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY K 363 " --> pdb=" O TRP K 352 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN K 402 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU K 375 " --> pdb=" O ARG K 400 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N ARG K 400 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N PHE K 377 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N VAL K 398 " --> pdb=" O PHE K 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL K 379 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 16.485A pdb=" N VAL K 396 " --> pdb=" O VAL K 379 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.453A pdb=" N GLU B 10 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.453A pdb=" N GLU B 10 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS B 96 " --> pdb=" O TRP B 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP B 118 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 98 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.648A pdb=" N LEU H 13 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 96 through 102 removed outlier: 3.621A pdb=" N GLY L 96 " --> pdb=" O THR L 449 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL L 445 " --> pdb=" O PHE L 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS L 102 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE L 443 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG L 420 " --> pdb=" O GLY L 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 115 through 124 removed outlier: 4.860A pdb=" N TRP L 115 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR L 138 " --> pdb=" O TRP L 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR L 117 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN L 136 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU L 119 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU L 134 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 157 " --> pdb=" O GLY L 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 158 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS L 172 " --> pdb=" O MET L 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 179 through 184 removed outlier: 3.620A pdb=" N SER L 179 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP L 197 " --> pdb=" O ASN L 200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP L 213 " --> pdb=" O PHE L 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR L 207 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU L 211 " --> pdb=" O TYR L 207 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 231 through 233 removed outlier: 3.735A pdb=" N VAL L 231 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU L 258 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 276 through 283 removed outlier: 5.435A pdb=" N GLU L 277 " --> pdb=" O ARG L 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG L 292 " --> pdb=" O GLU L 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 352 through 356 removed outlier: 4.842A pdb=" N TRP L 352 " --> pdb=" O GLY L 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY L 363 " --> pdb=" O TRP L 352 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN L 402 " --> pdb=" O GLY L 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU L 375 " --> pdb=" O ARG L 400 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N ARG L 400 " --> pdb=" O GLU L 375 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N PHE L 377 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N VAL L 398 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL L 379 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 16.485A pdb=" N VAL L 396 " --> pdb=" O VAL L 379 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU I 13 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1668 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: 3.82 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3289 1.30 - 1.44: 5731 1.44 - 1.57: 11592 1.57 - 1.70: 0 1.70 - 1.84: 144 Bond restraints: 20756 Sorted by residual: bond pdb=" CE1 HIS L 184 " pdb=" NE2 HIS L 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" CE1 HIS K 184 " pdb=" NE2 HIS K 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CE1 HIS G 184 " pdb=" NE2 HIS G 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CE1 HIS J 184 " pdb=" NE2 HIS J 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" C VAL J 317 " pdb=" O VAL J 317 " ideal model delta sigma weight residual 1.237 1.299 -0.062 9.90e-03 1.02e+04 3.91e+01 ... (remaining 20751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 19634 1.71 - 3.41: 6846 3.41 - 5.12: 1506 5.12 - 6.82: 160 6.82 - 8.53: 36 Bond angle restraints: 28182 Sorted by residual: angle pdb=" CA ASP L 125 " pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" CA ASP J 125 " pdb=" CB ASP J 125 " pdb=" CG ASP J 125 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP K 125 " pdb=" CB ASP K 125 " pdb=" CG ASP K 125 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" N SER K 180 " pdb=" CA SER K 180 " pdb=" C SER K 180 " ideal model delta sigma weight residual 108.60 116.46 -7.86 1.46e+00 4.69e-01 2.90e+01 ... (remaining 28177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 12551 21.62 - 43.23: 535 43.23 - 64.85: 85 64.85 - 86.47: 61 86.47 - 108.08: 28 Dihedral angle restraints: 13260 sinusoidal: 6116 harmonic: 7144 Sorted by residual: dihedral pdb=" CA VAL A 2 " pdb=" C VAL A 2 " pdb=" N HIS A 3 " pdb=" CA HIS A 3 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA VAL B 2 " pdb=" C VAL B 2 " pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta harmonic sigma weight residual 180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL C 2 " pdb=" C VAL C 2 " pdb=" N HIS C 3 " pdb=" CA HIS C 3 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 13257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1382 0.055 - 0.110: 1063 0.110 - 0.164: 602 0.164 - 0.219: 179 0.219 - 0.274: 66 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.28e+01 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.97e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.95e+01 ... (remaining 3289 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP J 115 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP J 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP J 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP J 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP K 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP K 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP K 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP K 115 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP K 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP K 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 115 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP K 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.12e+01 pdb=" CG TRP G 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP G 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP G 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP G 115 " 0.051 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3843 2.82 - 3.34: 18780 3.34 - 3.86: 32203 3.86 - 4.38: 41311 4.38 - 4.90: 68081 Nonbonded interactions: 164218 Sorted by model distance: nonbonded pdb=" O HIS L 347 " pdb="CA CA L2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS K 347 " pdb="CA CA K2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.303 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.303 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J2000 " model vdw 2.342 2.510 ... (remaining 164213 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' selection = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'G' and resid 82 through 501) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.840 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 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 : 0.017 0.193 20876 Z= 1.168 Angle : 1.799 12.359 28498 Z= 1.150 Chirality : 0.095 0.274 3292 Planarity : 0.011 0.068 3534 Dihedral : 14.521 108.083 8576 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.63 (0.15), residues: 2488 helix: -1.68 (0.62), residues: 24 sheet: 0.32 (0.16), residues: 980 loop : -0.92 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG L 156 TYR 0.058 0.012 TYR J 121 PHE 0.062 0.012 PHE L 205 TRP 0.113 0.014 TRP J 115 HIS 0.032 0.005 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.01636 (20756) covalent geometry : angle 1.75532 (28182) SS BOND : bond 0.08872 ( 44) SS BOND : angle 2.97254 ( 88) hydrogen bonds : bond 0.14918 ( 624) hydrogen bonds : angle 8.16693 ( 1668) link_ALPHA1-2 : bond 0.00279 ( 4) link_ALPHA1-2 : angle 5.04486 ( 12) link_ALPHA1-3 : bond 0.01567 ( 8) link_ALPHA1-3 : angle 3.88316 ( 24) link_ALPHA1-6 : bond 0.02024 ( 8) link_ALPHA1-6 : angle 3.12059 ( 24) link_BETA1-4 : bond 0.02144 ( 31) link_BETA1-4 : angle 4.18769 ( 93) link_BETA1-6 : bond 0.01864 ( 2) link_BETA1-6 : angle 4.41534 ( 6) link_NAG-ASN : bond 0.00626 ( 23) link_NAG-ASN : angle 5.33814 ( 69) *********************** 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 276 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ASP cc_start: 0.7076 (t0) cc_final: 0.6734 (t0) REVERT: F 85 ILE cc_start: 0.8678 (tt) cc_final: 0.8459 (tp) REVERT: A 10 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8290 (tp30) REVERT: A 73 ASP cc_start: 0.7079 (t0) cc_final: 0.6737 (t0) REVERT: D 85 ILE cc_start: 0.8673 (tt) cc_final: 0.8453 (tp) REVERT: B 73 ASP cc_start: 0.7074 (t0) cc_final: 0.6732 (t0) REVERT: H 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8458 (tp) REVERT: C 73 ASP cc_start: 0.7071 (t0) cc_final: 0.6728 (t0) REVERT: I 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8458 (tp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.7851 time to fit residues: 237.4944 Evaluate side-chains 204 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 ASN E 39 GLN E 43 GLN F 93 ASN J 147 ASN A 39 GLN A 43 GLN D 93 ASN K 147 ASN B 39 GLN B 43 GLN H 93 ASN L 147 ASN C 39 GLN C 43 GLN I 93 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.060701 restraints weight = 39374.686| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.90 r_work: 0.2791 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20876 Z= 0.145 Angle : 0.717 8.316 28498 Z= 0.368 Chirality : 0.047 0.164 3292 Planarity : 0.004 0.066 3534 Dihedral : 10.033 74.545 4264 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.10 % Allowed : 9.58 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.42 (0.16), residues: 2488 helix: -0.19 (0.98), residues: 24 sheet: 0.22 (0.15), residues: 1100 loop : -0.66 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 98 TYR 0.012 0.002 TYR F 49 PHE 0.014 0.002 PHE J 410 TRP 0.024 0.002 TRP J 178 HIS 0.004 0.001 HIS G 347 Details of bonding type rmsd covalent geometry : bond 0.00297 (20756) covalent geometry : angle 0.68837 (28182) SS BOND : bond 0.00499 ( 44) SS BOND : angle 1.06875 ( 88) hydrogen bonds : bond 0.04151 ( 624) hydrogen bonds : angle 6.61254 ( 1668) link_ALPHA1-2 : bond 0.00782 ( 4) link_ALPHA1-2 : angle 1.99942 ( 12) link_ALPHA1-3 : bond 0.01190 ( 8) link_ALPHA1-3 : angle 2.02591 ( 24) link_ALPHA1-6 : bond 0.00656 ( 8) link_ALPHA1-6 : angle 1.14769 ( 24) link_BETA1-4 : bond 0.00667 ( 31) link_BETA1-4 : angle 2.22480 ( 93) link_BETA1-6 : bond 0.01530 ( 2) link_BETA1-6 : angle 1.35861 ( 6) link_NAG-ASN : bond 0.00533 ( 23) link_NAG-ASN : angle 2.77110 ( 69) *********************** 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 276 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8783 (ttt) cc_final: 0.8510 (ttp) REVERT: E 10 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8282 (mp0) REVERT: E 23 LYS cc_start: 0.8633 (tttp) cc_final: 0.8424 (tttp) REVERT: E 73 ASP cc_start: 0.7243 (t0) cc_final: 0.6634 (t0) REVERT: F 61 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7443 (ptm160) REVERT: F 70 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7398 (mm-30) REVERT: F 79 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7821 (mp-120) REVERT: F 82 ASP cc_start: 0.8428 (m-30) cc_final: 0.7220 (m-30) REVERT: J 160 MET cc_start: 0.8787 (ttt) cc_final: 0.8514 (ttp) REVERT: A 10 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8269 (tp30) REVERT: A 23 LYS cc_start: 0.8642 (tttp) cc_final: 0.8298 (tttp) REVERT: A 65 GLN cc_start: 0.8235 (tt0) cc_final: 0.7679 (mt0) REVERT: A 73 ASP cc_start: 0.7255 (t0) cc_final: 0.6644 (t0) REVERT: D 61 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7506 (ptm160) REVERT: D 70 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7420 (mm-30) REVERT: D 79 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7827 (mp-120) REVERT: D 82 ASP cc_start: 0.8441 (m-30) cc_final: 0.7208 (m-30) REVERT: K 160 MET cc_start: 0.8782 (ttt) cc_final: 0.8522 (ttp) REVERT: B 10 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8275 (mp0) REVERT: B 23 LYS cc_start: 0.8639 (tttp) cc_final: 0.8433 (tttp) REVERT: B 73 ASP cc_start: 0.7200 (t0) cc_final: 0.6592 (t0) REVERT: H 61 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7399 (ptm160) REVERT: H 70 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7388 (mm-30) REVERT: H 79 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7816 (mp-120) REVERT: H 82 ASP cc_start: 0.8424 (m-30) cc_final: 0.7224 (m-30) REVERT: L 160 MET cc_start: 0.8792 (ttt) cc_final: 0.8520 (ttp) REVERT: C 10 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8295 (mp0) REVERT: C 23 LYS cc_start: 0.8634 (tttp) cc_final: 0.8424 (tttp) REVERT: C 73 ASP cc_start: 0.7231 (t0) cc_final: 0.6621 (t0) REVERT: I 61 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7394 (ptm160) REVERT: I 70 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7392 (mm-30) REVERT: I 79 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7818 (mp-120) REVERT: I 82 ASP cc_start: 0.8410 (m-30) cc_final: 0.7223 (m-30) outliers start: 45 outliers final: 4 residues processed: 255 average time/residue: 0.7409 time to fit residues: 208.0388 Evaluate side-chains 205 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 93 ASN A 39 GLN D 93 ASN B 39 GLN H 93 ASN C 39 GLN I 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.058080 restraints weight = 40114.126| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.94 r_work: 0.2737 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 20876 Z= 0.194 Angle : 0.701 7.644 28498 Z= 0.353 Chirality : 0.048 0.177 3292 Planarity : 0.004 0.044 3534 Dihedral : 8.657 64.098 4264 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.32 % Allowed : 9.67 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.47 (0.16), residues: 2488 helix: 0.13 (1.12), residues: 24 sheet: 0.29 (0.15), residues: 1076 loop : -0.78 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 18 TYR 0.019 0.002 TYR J 121 PHE 0.014 0.002 PHE J 410 TRP 0.021 0.002 TRP L 178 HIS 0.007 0.002 HIS J 184 Details of bonding type rmsd covalent geometry : bond 0.00464 (20756) covalent geometry : angle 0.67230 (28182) SS BOND : bond 0.00370 ( 44) SS BOND : angle 1.30941 ( 88) hydrogen bonds : bond 0.04055 ( 624) hydrogen bonds : angle 6.25769 ( 1668) link_ALPHA1-2 : bond 0.00304 ( 4) link_ALPHA1-2 : angle 2.33021 ( 12) link_ALPHA1-3 : bond 0.00768 ( 8) link_ALPHA1-3 : angle 1.93233 ( 24) link_ALPHA1-6 : bond 0.00493 ( 8) link_ALPHA1-6 : angle 1.41203 ( 24) link_BETA1-4 : bond 0.00585 ( 31) link_BETA1-4 : angle 2.11778 ( 93) link_BETA1-6 : bond 0.01215 ( 2) link_BETA1-6 : angle 1.09614 ( 6) link_NAG-ASN : bond 0.00322 ( 23) link_NAG-ASN : angle 2.61661 ( 69) *********************** 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 282 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8376 (mp0) REVERT: E 23 LYS cc_start: 0.8666 (tttp) cc_final: 0.8147 (tttp) REVERT: E 65 GLN cc_start: 0.8340 (tt0) cc_final: 0.7748 (mt0) REVERT: E 73 ASP cc_start: 0.7242 (t0) cc_final: 0.6627 (t0) REVERT: E 77 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7866 (p) REVERT: F 6 GLN cc_start: 0.7794 (tt0) cc_final: 0.7507 (tt0) REVERT: F 70 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7469 (mm-30) REVERT: F 82 ASP cc_start: 0.8520 (m-30) cc_final: 0.8232 (m-30) REVERT: A 10 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8384 (tp30) REVERT: A 23 LYS cc_start: 0.8666 (tttp) cc_final: 0.8220 (tttp) REVERT: A 65 GLN cc_start: 0.8330 (tt0) cc_final: 0.7764 (mt0) REVERT: A 73 ASP cc_start: 0.7245 (t0) cc_final: 0.6646 (t0) REVERT: D 6 GLN cc_start: 0.7778 (tt0) cc_final: 0.7505 (tt0) REVERT: D 70 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7469 (mm-30) REVERT: D 82 ASP cc_start: 0.8509 (m-30) cc_final: 0.8258 (m-30) REVERT: B 10 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8377 (mp0) REVERT: B 12 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8980 (mmmm) REVERT: B 23 LYS cc_start: 0.8673 (tttp) cc_final: 0.8158 (tttp) REVERT: B 65 GLN cc_start: 0.8335 (tt0) cc_final: 0.7741 (mt0) REVERT: B 73 ASP cc_start: 0.7224 (t0) cc_final: 0.6612 (t0) REVERT: B 77 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7865 (p) REVERT: H 70 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7470 (mm-30) REVERT: H 82 ASP cc_start: 0.8524 (m-30) cc_final: 0.8236 (m-30) REVERT: C 10 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8391 (mp0) REVERT: C 12 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8978 (mmmm) REVERT: C 23 LYS cc_start: 0.8653 (tttp) cc_final: 0.8123 (tttp) REVERT: C 65 GLN cc_start: 0.8329 (tt0) cc_final: 0.7740 (mt0) REVERT: C 73 ASP cc_start: 0.7236 (t0) cc_final: 0.6637 (t0) REVERT: C 77 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7863 (p) REVERT: I 6 GLN cc_start: 0.7791 (tt0) cc_final: 0.7516 (tt0) REVERT: I 70 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7461 (mm-30) REVERT: I 82 ASP cc_start: 0.8546 (m-30) cc_final: 0.8291 (m-30) outliers start: 71 outliers final: 20 residues processed: 256 average time/residue: 0.6884 time to fit residues: 194.5137 Evaluate side-chains 228 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057658 restraints weight = 40231.604| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.90 r_work: 0.2725 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20876 Z= 0.211 Angle : 0.682 7.499 28498 Z= 0.343 Chirality : 0.048 0.183 3292 Planarity : 0.004 0.036 3534 Dihedral : 7.684 59.725 4264 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 3.41 % Allowed : 10.09 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.43 (0.16), residues: 2488 helix: -0.07 (1.10), residues: 24 sheet: 0.41 (0.15), residues: 1064 loop : -0.85 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.017 0.002 TYR L 121 PHE 0.015 0.002 PHE J 410 TRP 0.022 0.002 TRP G 178 HIS 0.006 0.002 HIS K 184 Details of bonding type rmsd covalent geometry : bond 0.00504 (20756) covalent geometry : angle 0.65777 (28182) SS BOND : bond 0.00336 ( 44) SS BOND : angle 1.11287 ( 88) hydrogen bonds : bond 0.03918 ( 624) hydrogen bonds : angle 6.04908 ( 1668) link_ALPHA1-2 : bond 0.00296 ( 4) link_ALPHA1-2 : angle 2.48404 ( 12) link_ALPHA1-3 : bond 0.00697 ( 8) link_ALPHA1-3 : angle 2.06030 ( 24) link_ALPHA1-6 : bond 0.00457 ( 8) link_ALPHA1-6 : angle 1.41426 ( 24) link_BETA1-4 : bond 0.00507 ( 31) link_BETA1-4 : angle 1.87661 ( 93) link_BETA1-6 : bond 0.00928 ( 2) link_BETA1-6 : angle 1.05167 ( 6) link_NAG-ASN : bond 0.00336 ( 23) link_NAG-ASN : angle 2.42562 ( 69) *********************** 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 295 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 222 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (ttt) REVERT: E 10 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8539 (mp0) REVERT: E 23 LYS cc_start: 0.8697 (tttp) cc_final: 0.8184 (tttp) REVERT: E 39 GLN cc_start: 0.7649 (tt0) cc_final: 0.6997 (tp40) REVERT: E 65 GLN cc_start: 0.8353 (tt0) cc_final: 0.7766 (mm-40) REVERT: E 73 ASP cc_start: 0.7351 (t0) cc_final: 0.6741 (t0) REVERT: F 6 GLN cc_start: 0.7803 (tt0) cc_final: 0.7573 (tt0) REVERT: F 11 LEU cc_start: 0.8675 (tp) cc_final: 0.8394 (tt) REVERT: F 81 GLU cc_start: 0.8677 (pm20) cc_final: 0.8451 (pm20) REVERT: F 82 ASP cc_start: 0.8604 (m-30) cc_final: 0.8165 (m-30) REVERT: F 104 LYS cc_start: 0.8493 (tppt) cc_final: 0.8284 (tppt) REVERT: J 160 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8596 (ttt) REVERT: A 10 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8432 (tp30) REVERT: A 65 GLN cc_start: 0.8351 (tt0) cc_final: 0.7755 (mm-40) REVERT: A 73 ASP cc_start: 0.7379 (t0) cc_final: 0.6737 (t0) REVERT: A 87 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6970 (ptp-110) REVERT: A 90 ASP cc_start: 0.7976 (m-30) cc_final: 0.7652 (m-30) REVERT: D 6 GLN cc_start: 0.7757 (tt0) cc_final: 0.7515 (tt0) REVERT: D 11 LEU cc_start: 0.8639 (tp) cc_final: 0.8360 (tt) REVERT: D 81 GLU cc_start: 0.8626 (pm20) cc_final: 0.8402 (pm20) REVERT: D 82 ASP cc_start: 0.8602 (m-30) cc_final: 0.8168 (m-30) REVERT: D 104 LYS cc_start: 0.8487 (tppt) cc_final: 0.8276 (tppt) REVERT: K 160 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8601 (ttt) REVERT: B 10 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8487 (mp0) REVERT: B 23 LYS cc_start: 0.8706 (tttp) cc_final: 0.8203 (tttp) REVERT: B 39 GLN cc_start: 0.7670 (tt0) cc_final: 0.7014 (tp40) REVERT: B 65 GLN cc_start: 0.8347 (tt0) cc_final: 0.7758 (mm-40) REVERT: B 73 ASP cc_start: 0.7338 (t0) cc_final: 0.6729 (t0) REVERT: H 11 LEU cc_start: 0.8677 (tp) cc_final: 0.8397 (tt) REVERT: H 81 GLU cc_start: 0.8674 (pm20) cc_final: 0.8450 (pm20) REVERT: H 82 ASP cc_start: 0.8603 (m-30) cc_final: 0.8170 (m-30) REVERT: H 104 LYS cc_start: 0.8505 (tppt) cc_final: 0.8294 (tppt) REVERT: L 160 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8608 (ttt) REVERT: C 10 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8512 (mp0) REVERT: C 23 LYS cc_start: 0.8691 (tttp) cc_final: 0.8172 (tttp) REVERT: C 39 GLN cc_start: 0.7633 (tt0) cc_final: 0.6985 (tp40) REVERT: C 65 GLN cc_start: 0.8350 (tt0) cc_final: 0.7762 (mm-40) REVERT: C 73 ASP cc_start: 0.7352 (t0) cc_final: 0.6740 (t0) REVERT: I 6 GLN cc_start: 0.7746 (tt0) cc_final: 0.7503 (tt0) REVERT: I 11 LEU cc_start: 0.8655 (tp) cc_final: 0.8364 (tt) REVERT: I 81 GLU cc_start: 0.8632 (pm20) cc_final: 0.8409 (pm20) REVERT: I 82 ASP cc_start: 0.8589 (m-30) cc_final: 0.8155 (m-30) REVERT: I 104 LYS cc_start: 0.8484 (tppt) cc_final: 0.8274 (tppt) outliers start: 73 outliers final: 17 residues processed: 261 average time/residue: 0.6882 time to fit residues: 198.4506 Evaluate side-chains 229 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS J 347 HIS A 39 GLN K 347 HIS H 6 GLN L 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058424 restraints weight = 39917.299| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.90 r_work: 0.2746 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 20876 Z= 0.150 Angle : 0.643 8.992 28498 Z= 0.320 Chirality : 0.046 0.184 3292 Planarity : 0.004 0.046 3534 Dihedral : 7.167 57.127 4264 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 2.57 % Allowed : 10.79 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.14 (1.07), residues: 24 sheet: 0.49 (0.16), residues: 1072 loop : -0.77 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 63 TYR 0.018 0.001 TYR D 49 PHE 0.013 0.002 PHE L 410 TRP 0.021 0.001 TRP J 178 HIS 0.004 0.001 HIS L 347 Details of bonding type rmsd covalent geometry : bond 0.00352 (20756) covalent geometry : angle 0.62147 (28182) SS BOND : bond 0.00238 ( 44) SS BOND : angle 0.93998 ( 88) hydrogen bonds : bond 0.03524 ( 624) hydrogen bonds : angle 5.87990 ( 1668) link_ALPHA1-2 : bond 0.00397 ( 4) link_ALPHA1-2 : angle 2.41447 ( 12) link_ALPHA1-3 : bond 0.00824 ( 8) link_ALPHA1-3 : angle 1.85648 ( 24) link_ALPHA1-6 : bond 0.00506 ( 8) link_ALPHA1-6 : angle 1.38473 ( 24) link_BETA1-4 : bond 0.00531 ( 31) link_BETA1-4 : angle 1.63895 ( 93) link_BETA1-6 : bond 0.00845 ( 2) link_BETA1-6 : angle 1.08023 ( 6) link_NAG-ASN : bond 0.00314 ( 23) link_NAG-ASN : angle 2.26009 ( 69) *********************** 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 279 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8499 (mp0) REVERT: E 23 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (tptt) REVERT: E 46 GLU cc_start: 0.8671 (tt0) cc_final: 0.8051 (tt0) REVERT: E 65 GLN cc_start: 0.8382 (tt0) cc_final: 0.7833 (mm-40) REVERT: E 73 ASP cc_start: 0.7341 (t0) cc_final: 0.6696 (t0) REVERT: E 77 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7804 (p) REVERT: F 11 LEU cc_start: 0.8700 (tp) cc_final: 0.8439 (tt) REVERT: F 39 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8726 (mttm) REVERT: F 70 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7825 (mm-30) REVERT: F 81 GLU cc_start: 0.8644 (pm20) cc_final: 0.8419 (pm20) REVERT: F 82 ASP cc_start: 0.8589 (m-30) cc_final: 0.8214 (m-30) REVERT: F 104 LYS cc_start: 0.8553 (tppt) cc_final: 0.8177 (tppt) REVERT: A 10 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8439 (tp30) REVERT: A 23 LYS cc_start: 0.8901 (tttp) cc_final: 0.8573 (tttp) REVERT: A 46 GLU cc_start: 0.8656 (tt0) cc_final: 0.8160 (tt0) REVERT: A 65 GLN cc_start: 0.8349 (tt0) cc_final: 0.7778 (mm-40) REVERT: A 73 ASP cc_start: 0.7362 (t0) cc_final: 0.6769 (t0) REVERT: A 77 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 90 ASP cc_start: 0.7679 (m-30) cc_final: 0.7252 (m-30) REVERT: D 11 LEU cc_start: 0.8688 (tp) cc_final: 0.8432 (tt) REVERT: D 39 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8721 (mttm) REVERT: D 61 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8327 (ptm160) REVERT: D 70 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 81 GLU cc_start: 0.8634 (pm20) cc_final: 0.8384 (pm20) REVERT: D 82 ASP cc_start: 0.8613 (m-30) cc_final: 0.8104 (m-30) REVERT: D 104 LYS cc_start: 0.8574 (tppt) cc_final: 0.8169 (tppt) REVERT: B 10 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8505 (mp0) REVERT: B 23 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (tptt) REVERT: B 46 GLU cc_start: 0.8651 (tt0) cc_final: 0.8227 (tt0) REVERT: B 65 GLN cc_start: 0.8403 (tt0) cc_final: 0.7840 (mm-40) REVERT: B 73 ASP cc_start: 0.7349 (t0) cc_final: 0.6704 (t0) REVERT: B 77 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7812 (p) REVERT: H 11 LEU cc_start: 0.8701 (tp) cc_final: 0.8445 (tt) REVERT: H 70 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7823 (mm-30) REVERT: H 81 GLU cc_start: 0.8641 (pm20) cc_final: 0.8417 (pm20) REVERT: H 82 ASP cc_start: 0.8590 (m-30) cc_final: 0.8219 (m-30) REVERT: H 104 LYS cc_start: 0.8590 (tppt) cc_final: 0.8182 (tppt) REVERT: C 10 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8519 (mp0) REVERT: C 23 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8641 (tptt) REVERT: C 46 GLU cc_start: 0.8661 (tt0) cc_final: 0.8203 (tt0) REVERT: C 65 GLN cc_start: 0.8399 (tt0) cc_final: 0.7839 (mm-40) REVERT: C 73 ASP cc_start: 0.7343 (t0) cc_final: 0.6697 (t0) REVERT: C 77 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7805 (p) REVERT: I 11 LEU cc_start: 0.8677 (tp) cc_final: 0.8396 (tt) REVERT: I 39 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8730 (mttm) REVERT: I 70 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7806 (mm-30) REVERT: I 81 GLU cc_start: 0.8642 (pm20) cc_final: 0.8383 (pm20) REVERT: I 82 ASP cc_start: 0.8632 (m-30) cc_final: 0.8255 (m-30) REVERT: I 104 LYS cc_start: 0.8577 (tppt) cc_final: 0.8170 (tppt) outliers start: 55 outliers final: 18 residues processed: 255 average time/residue: 0.6918 time to fit residues: 195.6438 Evaluate side-chains 241 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 243 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN L 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.056019 restraints weight = 40417.268| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.96 r_work: 0.2692 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 20876 Z= 0.301 Angle : 0.753 9.857 28498 Z= 0.374 Chirality : 0.050 0.179 3292 Planarity : 0.005 0.045 3534 Dihedral : 7.788 61.349 4264 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 3.41 % Allowed : 11.03 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.60 (0.16), residues: 2488 helix: -0.17 (1.14), residues: 24 sheet: 0.34 (0.16), residues: 1048 loop : -0.98 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 45 TYR 0.021 0.002 TYR J 121 PHE 0.018 0.002 PHE G 410 TRP 0.020 0.002 TRP L 178 HIS 0.008 0.002 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00724 (20756) covalent geometry : angle 0.72650 (28182) SS BOND : bond 0.00384 ( 44) SS BOND : angle 1.18008 ( 88) hydrogen bonds : bond 0.04250 ( 624) hydrogen bonds : angle 5.98724 ( 1668) link_ALPHA1-2 : bond 0.00075 ( 4) link_ALPHA1-2 : angle 2.75604 ( 12) link_ALPHA1-3 : bond 0.00387 ( 8) link_ALPHA1-3 : angle 2.41541 ( 24) link_ALPHA1-6 : bond 0.00285 ( 8) link_ALPHA1-6 : angle 1.52731 ( 24) link_BETA1-4 : bond 0.00460 ( 31) link_BETA1-4 : angle 1.96723 ( 93) link_BETA1-6 : bond 0.00837 ( 2) link_BETA1-6 : angle 1.04057 ( 6) link_NAG-ASN : bond 0.00500 ( 23) link_NAG-ASN : angle 2.72306 ( 69) *********************** 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 293 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 220 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8632 (ttt) REVERT: E 10 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8504 (mp0) REVERT: E 23 LYS cc_start: 0.8862 (tttp) cc_final: 0.8587 (tttp) REVERT: E 46 GLU cc_start: 0.8689 (tt0) cc_final: 0.8267 (tt0) REVERT: E 65 GLN cc_start: 0.8581 (tt0) cc_final: 0.8007 (mm-40) REVERT: E 73 ASP cc_start: 0.7465 (t0) cc_final: 0.6878 (t0) REVERT: E 77 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7964 (p) REVERT: E 87 ARG cc_start: 0.7496 (mtm110) cc_final: 0.6934 (ptp-110) REVERT: E 90 ASP cc_start: 0.8037 (m-30) cc_final: 0.7771 (m-30) REVERT: F 81 GLU cc_start: 0.8718 (pm20) cc_final: 0.8420 (pm20) REVERT: F 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.7895 (m-30) REVERT: F 104 LYS cc_start: 0.8618 (tppt) cc_final: 0.8412 (tppt) REVERT: J 160 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8622 (ttt) REVERT: A 10 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8443 (tp30) REVERT: A 23 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8553 (tttp) REVERT: A 39 GLN cc_start: 0.7608 (tt0) cc_final: 0.6930 (tp40) REVERT: A 46 GLU cc_start: 0.8643 (tt0) cc_final: 0.8111 (tt0) REVERT: A 65 GLN cc_start: 0.8547 (tt0) cc_final: 0.7967 (mm-40) REVERT: A 73 ASP cc_start: 0.7485 (t0) cc_final: 0.6910 (t0) REVERT: A 107 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: D 61 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: D 81 GLU cc_start: 0.8705 (pm20) cc_final: 0.8398 (pm20) REVERT: D 82 ASP cc_start: 0.8724 (m-30) cc_final: 0.7797 (m-30) REVERT: D 104 LYS cc_start: 0.8617 (tppt) cc_final: 0.8409 (tppt) REVERT: K 160 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8633 (ttt) REVERT: B 10 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8511 (mp0) REVERT: B 23 LYS cc_start: 0.8871 (tttp) cc_final: 0.8592 (tttp) REVERT: B 46 GLU cc_start: 0.8688 (tt0) cc_final: 0.8169 (tt0) REVERT: B 65 GLN cc_start: 0.8560 (tt0) cc_final: 0.7940 (mm-40) REVERT: B 73 ASP cc_start: 0.7461 (t0) cc_final: 0.6871 (t0) REVERT: B 77 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 87 ARG cc_start: 0.7499 (mtm110) cc_final: 0.6927 (ptp-110) REVERT: B 90 ASP cc_start: 0.8056 (m-30) cc_final: 0.7785 (m-30) REVERT: H 6 GLN cc_start: 0.7944 (tt0) cc_final: 0.7738 (tt0) REVERT: H 81 GLU cc_start: 0.8798 (pm20) cc_final: 0.8465 (pm20) REVERT: H 82 ASP cc_start: 0.8749 (m-30) cc_final: 0.7807 (m-30) REVERT: H 104 LYS cc_start: 0.8640 (tppt) cc_final: 0.8436 (tppt) REVERT: L 160 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8640 (ttt) REVERT: C 10 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8530 (mp0) REVERT: C 23 LYS cc_start: 0.8831 (tttp) cc_final: 0.8515 (tttp) REVERT: C 46 GLU cc_start: 0.8744 (tt0) cc_final: 0.8241 (tt0) REVERT: C 65 GLN cc_start: 0.8553 (tt0) cc_final: 0.7933 (mm-40) REVERT: C 73 ASP cc_start: 0.7459 (t0) cc_final: 0.6871 (t0) REVERT: C 77 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7966 (p) REVERT: C 87 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6931 (ptp-110) REVERT: C 90 ASP cc_start: 0.8031 (m-30) cc_final: 0.7763 (m-30) REVERT: I 81 GLU cc_start: 0.8714 (pm20) cc_final: 0.8428 (pm20) REVERT: I 82 ASP cc_start: 0.8657 (m-30) cc_final: 0.7720 (m-30) outliers start: 73 outliers final: 27 residues processed: 268 average time/residue: 0.6797 time to fit residues: 201.6536 Evaluate side-chains 249 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 92 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 92 ASN L 226 GLN I 32 ASN I 92 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056477 restraints weight = 40290.300| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.94 r_work: 0.2701 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 20876 Z= 0.261 Angle : 0.734 10.867 28498 Z= 0.363 Chirality : 0.048 0.176 3292 Planarity : 0.005 0.058 3534 Dihedral : 7.685 60.539 4264 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.06 % Favored : 95.78 % Rotamer: Outliers : 2.85 % Allowed : 12.71 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.71 (0.16), residues: 2488 helix: -0.31 (1.10), residues: 24 sheet: 0.31 (0.16), residues: 1048 loop : -1.10 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 63 TYR 0.022 0.002 TYR D 49 PHE 0.017 0.002 PHE L 410 TRP 0.022 0.002 TRP L 178 HIS 0.006 0.001 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00627 (20756) covalent geometry : angle 0.70939 (28182) SS BOND : bond 0.00334 ( 44) SS BOND : angle 1.28154 ( 88) hydrogen bonds : bond 0.04033 ( 624) hydrogen bonds : angle 5.86706 ( 1668) link_ALPHA1-2 : bond 0.00201 ( 4) link_ALPHA1-2 : angle 2.74370 ( 12) link_ALPHA1-3 : bond 0.00487 ( 8) link_ALPHA1-3 : angle 2.21962 ( 24) link_ALPHA1-6 : bond 0.00332 ( 8) link_ALPHA1-6 : angle 1.47987 ( 24) link_BETA1-4 : bond 0.00470 ( 31) link_BETA1-4 : angle 1.82155 ( 93) link_BETA1-6 : bond 0.00793 ( 2) link_BETA1-6 : angle 1.00890 ( 6) link_NAG-ASN : bond 0.00446 ( 23) link_NAG-ASN : angle 2.54942 ( 69) *********************** 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 273 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 128 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8118 (ptmt) REVERT: E 10 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8555 (mp0) REVERT: E 23 LYS cc_start: 0.8847 (tttp) cc_final: 0.8518 (tttp) REVERT: E 46 GLU cc_start: 0.8779 (tt0) cc_final: 0.8217 (tt0) REVERT: E 65 GLN cc_start: 0.8647 (tt0) cc_final: 0.7969 (mm-40) REVERT: E 73 ASP cc_start: 0.7521 (t0) cc_final: 0.6935 (t0) REVERT: E 77 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (p) REVERT: E 107 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8845 (m-30) REVERT: F 39 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8724 (mttm) REVERT: F 81 GLU cc_start: 0.8784 (pm20) cc_final: 0.8533 (pm20) REVERT: F 82 ASP cc_start: 0.8834 (m-30) cc_final: 0.8126 (m-30) REVERT: J 128 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8089 (ptmt) REVERT: A 10 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8444 (tp30) REVERT: A 46 GLU cc_start: 0.8755 (tt0) cc_final: 0.8173 (tt0) REVERT: A 65 GLN cc_start: 0.8669 (tt0) cc_final: 0.7983 (mm-40) REVERT: A 73 ASP cc_start: 0.7546 (t0) cc_final: 0.6976 (t0) REVERT: A 107 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8819 (m-30) REVERT: D 39 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8705 (mttm) REVERT: D 81 GLU cc_start: 0.8785 (pm20) cc_final: 0.8511 (pm20) REVERT: D 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.7861 (m-30) REVERT: B 10 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8538 (mp0) REVERT: B 23 LYS cc_start: 0.8853 (tttp) cc_final: 0.8523 (tttp) REVERT: B 46 GLU cc_start: 0.8776 (tt0) cc_final: 0.8241 (tt0) REVERT: B 65 GLN cc_start: 0.8644 (tt0) cc_final: 0.7967 (mm-40) REVERT: B 73 ASP cc_start: 0.7521 (t0) cc_final: 0.6934 (t0) REVERT: B 77 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 107 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: H 81 GLU cc_start: 0.8854 (pm20) cc_final: 0.8543 (pm20) REVERT: H 82 ASP cc_start: 0.8786 (m-30) cc_final: 0.7853 (m-30) REVERT: C 10 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8562 (mp0) REVERT: C 23 LYS cc_start: 0.8847 (tttp) cc_final: 0.8508 (tttp) REVERT: C 46 GLU cc_start: 0.8762 (tt0) cc_final: 0.8200 (tt0) REVERT: C 65 GLN cc_start: 0.8649 (tt0) cc_final: 0.7967 (mm-40) REVERT: C 73 ASP cc_start: 0.7527 (t0) cc_final: 0.6941 (t0) REVERT: C 77 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 107 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8848 (m-30) REVERT: I 39 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8718 (mttm) REVERT: I 81 GLU cc_start: 0.8774 (pm20) cc_final: 0.8536 (pm20) REVERT: I 82 ASP cc_start: 0.8580 (m-30) cc_final: 0.7589 (m-30) REVERT: I 104 LYS cc_start: 0.8120 (tppt) cc_final: 0.7891 (tppt) outliers start: 61 outliers final: 20 residues processed: 251 average time/residue: 0.6852 time to fit residues: 190.1560 Evaluate side-chains 235 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 237 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN G 441 ASN F 32 ASN F 92 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 ASN H 6 GLN L 441 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058435 restraints weight = 39876.933| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.93 r_work: 0.2747 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20876 Z= 0.127 Angle : 0.661 11.266 28498 Z= 0.322 Chirality : 0.045 0.184 3292 Planarity : 0.005 0.050 3534 Dihedral : 6.856 51.861 4264 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 2.29 % Allowed : 13.64 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.53 (0.16), residues: 2488 helix: -0.31 (1.04), residues: 24 sheet: 0.39 (0.16), residues: 1060 loop : -0.95 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 45 TYR 0.010 0.001 TYR L 121 PHE 0.012 0.002 PHE L 354 TRP 0.024 0.001 TRP K 178 HIS 0.003 0.001 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00291 (20756) covalent geometry : angle 0.64321 (28182) SS BOND : bond 0.00251 ( 44) SS BOND : angle 0.88714 ( 88) hydrogen bonds : bond 0.03317 ( 624) hydrogen bonds : angle 5.63364 ( 1668) link_ALPHA1-2 : bond 0.00499 ( 4) link_ALPHA1-2 : angle 2.47835 ( 12) link_ALPHA1-3 : bond 0.01008 ( 8) link_ALPHA1-3 : angle 1.80034 ( 24) link_ALPHA1-6 : bond 0.00561 ( 8) link_ALPHA1-6 : angle 1.36884 ( 24) link_BETA1-4 : bond 0.00565 ( 31) link_BETA1-4 : angle 1.48142 ( 93) link_BETA1-6 : bond 0.00788 ( 2) link_BETA1-6 : angle 1.15247 ( 6) link_NAG-ASN : bond 0.00326 ( 23) link_NAG-ASN : angle 2.12017 ( 69) *********************** 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 266 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8563 (mp0) REVERT: E 23 LYS cc_start: 0.8801 (tttp) cc_final: 0.8570 (tttp) REVERT: E 46 GLU cc_start: 0.8691 (tt0) cc_final: 0.8198 (tt0) REVERT: E 65 GLN cc_start: 0.8479 (tt0) cc_final: 0.7927 (mm-40) REVERT: E 73 ASP cc_start: 0.7477 (t0) cc_final: 0.6872 (t0) REVERT: F 79 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8239 (mm110) REVERT: F 81 GLU cc_start: 0.8774 (pm20) cc_final: 0.8547 (pm20) REVERT: F 82 ASP cc_start: 0.8825 (m-30) cc_final: 0.8485 (m-30) REVERT: A 10 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8452 (tp30) REVERT: A 23 LYS cc_start: 0.8855 (tttp) cc_final: 0.8536 (tptt) REVERT: A 46 GLU cc_start: 0.8637 (tt0) cc_final: 0.8054 (tt0) REVERT: A 65 GLN cc_start: 0.8457 (tt0) cc_final: 0.7929 (mm-40) REVERT: A 73 ASP cc_start: 0.7520 (t0) cc_final: 0.6936 (t0) REVERT: D 18 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8736 (tpp80) REVERT: D 79 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7811 (mp-120) REVERT: D 81 GLU cc_start: 0.8729 (pm20) cc_final: 0.8483 (pm20) REVERT: D 82 ASP cc_start: 0.8571 (m-30) cc_final: 0.7763 (m-30) REVERT: B 10 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8528 (mp0) REVERT: B 23 LYS cc_start: 0.8809 (tttp) cc_final: 0.8581 (tttp) REVERT: B 46 GLU cc_start: 0.8612 (tt0) cc_final: 0.8098 (tt0) REVERT: B 65 GLN cc_start: 0.8467 (tt0) cc_final: 0.7909 (mm-40) REVERT: B 73 ASP cc_start: 0.7473 (t0) cc_final: 0.6861 (t0) REVERT: H 6 GLN cc_start: 0.7794 (tt0) cc_final: 0.7356 (tt0) REVERT: H 79 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8275 (mm110) REVERT: H 81 GLU cc_start: 0.8829 (pm20) cc_final: 0.8520 (pm20) REVERT: H 82 ASP cc_start: 0.8678 (m-30) cc_final: 0.8052 (m-30) REVERT: C 10 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8553 (mp0) REVERT: C 23 LYS cc_start: 0.8794 (tttp) cc_final: 0.8557 (tttp) REVERT: C 46 GLU cc_start: 0.8686 (tt0) cc_final: 0.8134 (tt0) REVERT: C 65 GLN cc_start: 0.8481 (tt0) cc_final: 0.7925 (mm-40) REVERT: C 73 ASP cc_start: 0.7478 (t0) cc_final: 0.6872 (t0) REVERT: I 18 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8729 (tpp80) REVERT: I 39 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8723 (mttm) REVERT: I 79 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7849 (mp-120) REVERT: I 81 GLU cc_start: 0.8760 (pm20) cc_final: 0.8532 (pm20) REVERT: I 82 ASP cc_start: 0.8416 (m-30) cc_final: 0.7515 (m-30) outliers start: 49 outliers final: 25 residues processed: 244 average time/residue: 0.6587 time to fit residues: 177.9734 Evaluate side-chains 233 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057880 restraints weight = 39841.230| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.91 r_work: 0.2736 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20876 Z= 0.167 Angle : 0.687 11.336 28498 Z= 0.336 Chirality : 0.046 0.188 3292 Planarity : 0.005 0.059 3534 Dihedral : 6.823 51.536 4264 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 1.68 % Allowed : 15.00 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.55 (0.16), residues: 2488 helix: -0.27 (1.06), residues: 24 sheet: 0.42 (0.16), residues: 1060 loop : -0.99 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 63 TYR 0.020 0.001 TYR I 49 PHE 0.013 0.002 PHE J 410 TRP 0.021 0.001 TRP J 178 HIS 0.004 0.001 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00399 (20756) covalent geometry : angle 0.66863 (28182) SS BOND : bond 0.00273 ( 44) SS BOND : angle 0.91986 ( 88) hydrogen bonds : bond 0.03492 ( 624) hydrogen bonds : angle 5.63069 ( 1668) link_ALPHA1-2 : bond 0.00339 ( 4) link_ALPHA1-2 : angle 2.50364 ( 12) link_ALPHA1-3 : bond 0.00717 ( 8) link_ALPHA1-3 : angle 1.92670 ( 24) link_ALPHA1-6 : bond 0.00470 ( 8) link_ALPHA1-6 : angle 1.43281 ( 24) link_BETA1-4 : bond 0.00509 ( 31) link_BETA1-4 : angle 1.58050 ( 93) link_BETA1-6 : bond 0.00707 ( 2) link_BETA1-6 : angle 1.08565 ( 6) link_NAG-ASN : bond 0.00313 ( 23) link_NAG-ASN : angle 2.22616 ( 69) *********************** 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 247 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8545 (mp0) REVERT: E 23 LYS cc_start: 0.8793 (tttp) cc_final: 0.8561 (tttp) REVERT: E 46 GLU cc_start: 0.8749 (tt0) cc_final: 0.8097 (tt0) REVERT: E 65 GLN cc_start: 0.8512 (tt0) cc_final: 0.7932 (mm-40) REVERT: E 73 ASP cc_start: 0.7495 (t0) cc_final: 0.6902 (t0) REVERT: F 4 MET cc_start: 0.7869 (tpp) cc_final: 0.7471 (mmm) REVERT: F 79 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8267 (mm110) REVERT: F 81 GLU cc_start: 0.8822 (pm20) cc_final: 0.8497 (pm20) REVERT: F 82 ASP cc_start: 0.8738 (m-30) cc_final: 0.8191 (m-30) REVERT: A 10 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8402 (tp30) REVERT: A 46 GLU cc_start: 0.8708 (tt0) cc_final: 0.8047 (tt0) REVERT: A 65 GLN cc_start: 0.8567 (tt0) cc_final: 0.8012 (mm-40) REVERT: A 73 ASP cc_start: 0.7535 (t0) cc_final: 0.6985 (t0) REVERT: D 18 ARG cc_start: 0.9150 (tpp80) cc_final: 0.8809 (tpp80) REVERT: D 79 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7867 (mm110) REVERT: D 81 GLU cc_start: 0.8776 (pm20) cc_final: 0.8460 (pm20) REVERT: D 82 ASP cc_start: 0.8537 (m-30) cc_final: 0.7551 (m-30) REVERT: B 10 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8531 (mp0) REVERT: B 23 LYS cc_start: 0.8798 (tttp) cc_final: 0.8568 (tttp) REVERT: B 46 GLU cc_start: 0.8730 (tt0) cc_final: 0.8096 (tt0) REVERT: B 65 GLN cc_start: 0.8531 (tt0) cc_final: 0.7954 (mm-40) REVERT: B 73 ASP cc_start: 0.7506 (t0) cc_final: 0.6899 (t0) REVERT: H 4 MET cc_start: 0.7771 (tpp) cc_final: 0.7445 (mmm) REVERT: H 18 ARG cc_start: 0.9112 (tpp80) cc_final: 0.8727 (tpp80) REVERT: H 61 ARG cc_start: 0.8882 (mtm110) cc_final: 0.8650 (mtm110) REVERT: H 79 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8234 (mp-120) REVERT: H 81 GLU cc_start: 0.8817 (pm20) cc_final: 0.8491 (pm20) REVERT: H 82 ASP cc_start: 0.8620 (m-30) cc_final: 0.8274 (m-30) REVERT: C 10 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8549 (mp0) REVERT: C 23 LYS cc_start: 0.8788 (tttp) cc_final: 0.8549 (tttp) REVERT: C 46 GLU cc_start: 0.8739 (tt0) cc_final: 0.8084 (tt0) REVERT: C 65 GLN cc_start: 0.8508 (tt0) cc_final: 0.7926 (mm-40) REVERT: C 73 ASP cc_start: 0.7490 (t0) cc_final: 0.6894 (t0) REVERT: I 4 MET cc_start: 0.7860 (tpp) cc_final: 0.7464 (mmm) REVERT: I 18 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8791 (tpp80) REVERT: I 39 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8715 (mttm) REVERT: I 79 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7803 (mp-120) REVERT: I 81 GLU cc_start: 0.8738 (pm20) cc_final: 0.8518 (pm20) REVERT: I 82 ASP cc_start: 0.8563 (m-30) cc_final: 0.7698 (m-30) outliers start: 36 outliers final: 25 residues processed: 236 average time/residue: 0.6830 time to fit residues: 178.4105 Evaluate side-chains 230 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057606 restraints weight = 40215.198| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.94 r_work: 0.2730 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20876 Z= 0.182 Angle : 0.692 11.620 28498 Z= 0.336 Chirality : 0.046 0.190 3292 Planarity : 0.004 0.058 3534 Dihedral : 6.848 51.668 4264 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 1.54 % Allowed : 15.19 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.59 (0.16), residues: 2488 helix: -0.26 (1.06), residues: 24 sheet: 0.36 (0.16), residues: 1060 loop : -1.00 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 45 TYR 0.021 0.001 TYR F 49 PHE 0.014 0.002 PHE K 410 TRP 0.020 0.001 TRP J 178 HIS 0.004 0.001 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00436 (20756) covalent geometry : angle 0.67256 (28182) SS BOND : bond 0.00294 ( 44) SS BOND : angle 0.93896 ( 88) hydrogen bonds : bond 0.03568 ( 624) hydrogen bonds : angle 5.63473 ( 1668) link_ALPHA1-2 : bond 0.00320 ( 4) link_ALPHA1-2 : angle 2.54287 ( 12) link_ALPHA1-3 : bond 0.00682 ( 8) link_ALPHA1-3 : angle 1.98473 ( 24) link_ALPHA1-6 : bond 0.00442 ( 8) link_ALPHA1-6 : angle 1.43619 ( 24) link_BETA1-4 : bond 0.00503 ( 31) link_BETA1-4 : angle 1.59426 ( 93) link_BETA1-6 : bond 0.00692 ( 2) link_BETA1-6 : angle 1.06862 ( 6) link_NAG-ASN : bond 0.00322 ( 23) link_NAG-ASN : angle 2.25212 ( 69) ********************** 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 243 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8551 (mp0) REVERT: E 23 LYS cc_start: 0.8779 (tttp) cc_final: 0.8413 (tttp) REVERT: E 46 GLU cc_start: 0.8745 (tt0) cc_final: 0.8188 (tt0) REVERT: E 65 GLN cc_start: 0.8530 (tt0) cc_final: 0.7956 (mm-40) REVERT: E 73 ASP cc_start: 0.7465 (t0) cc_final: 0.6881 (t0) REVERT: F 4 MET cc_start: 0.7853 (tpp) cc_final: 0.7538 (mmm) REVERT: F 79 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8242 (mm110) REVERT: F 81 GLU cc_start: 0.8823 (pm20) cc_final: 0.8503 (pm20) REVERT: F 82 ASP cc_start: 0.8705 (m-30) cc_final: 0.8207 (m-30) REVERT: A 10 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8435 (tp30) REVERT: A 46 GLU cc_start: 0.8711 (tt0) cc_final: 0.8194 (tt0) REVERT: A 65 GLN cc_start: 0.8532 (tt0) cc_final: 0.7980 (mm-40) REVERT: A 73 ASP cc_start: 0.7548 (t0) cc_final: 0.7000 (t0) REVERT: D 4 MET cc_start: 0.7741 (tpp) cc_final: 0.7420 (mmm) REVERT: D 18 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8837 (tpp80) REVERT: D 79 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7874 (mm110) REVERT: D 81 GLU cc_start: 0.8784 (pm20) cc_final: 0.8477 (pm20) REVERT: D 82 ASP cc_start: 0.8640 (m-30) cc_final: 0.7675 (m-30) REVERT: B 10 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8555 (mp0) REVERT: B 23 LYS cc_start: 0.8789 (tttp) cc_final: 0.8554 (tttp) REVERT: B 46 GLU cc_start: 0.8727 (tt0) cc_final: 0.8135 (tt0) REVERT: B 65 GLN cc_start: 0.8531 (tt0) cc_final: 0.7954 (mm-40) REVERT: B 73 ASP cc_start: 0.7540 (t0) cc_final: 0.6915 (t0) REVERT: H 4 MET cc_start: 0.7769 (tpp) cc_final: 0.7463 (mmm) REVERT: H 18 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8790 (tpp80) REVERT: H 79 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8220 (mm110) REVERT: H 81 GLU cc_start: 0.8809 (pm20) cc_final: 0.8479 (pm20) REVERT: H 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.8194 (m-30) REVERT: C 10 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8573 (mp0) REVERT: C 23 LYS cc_start: 0.8782 (tttp) cc_final: 0.8529 (tttp) REVERT: C 46 GLU cc_start: 0.8727 (tt0) cc_final: 0.8166 (tt0) REVERT: C 65 GLN cc_start: 0.8537 (tt0) cc_final: 0.7962 (mm-40) REVERT: C 73 ASP cc_start: 0.7461 (t0) cc_final: 0.6876 (t0) REVERT: I 4 MET cc_start: 0.7853 (tpp) cc_final: 0.7545 (mmm) REVERT: I 18 ARG cc_start: 0.9189 (tpp80) cc_final: 0.8866 (tpp80) REVERT: I 54 ARG cc_start: 0.8071 (pmm-80) cc_final: 0.7777 (ptp90) REVERT: I 79 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7775 (mm110) REVERT: I 81 GLU cc_start: 0.8750 (pm20) cc_final: 0.8516 (pm20) REVERT: I 82 ASP cc_start: 0.8622 (m-30) cc_final: 0.7719 (m-30) outliers start: 33 outliers final: 25 residues processed: 236 average time/residue: 0.7045 time to fit residues: 184.1767 Evaluate side-chains 232 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.088259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057055 restraints weight = 40350.264| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.94 r_work: 0.2717 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20876 Z= 0.216 Angle : 0.721 11.680 28498 Z= 0.351 Chirality : 0.047 0.191 3292 Planarity : 0.005 0.068 3534 Dihedral : 7.042 53.837 4264 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.70 % Favored : 95.14 % Rotamer: Outliers : 1.50 % Allowed : 15.28 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.66 (0.16), residues: 2488 helix: -0.25 (1.08), residues: 24 sheet: 0.33 (0.16), residues: 1060 loop : -1.07 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 63 TYR 0.023 0.002 TYR I 49 PHE 0.015 0.002 PHE L 410 TRP 0.019 0.001 TRP J 178 HIS 0.005 0.001 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00517 (20756) covalent geometry : angle 0.70136 (28182) SS BOND : bond 0.00313 ( 44) SS BOND : angle 0.99526 ( 88) hydrogen bonds : bond 0.03741 ( 624) hydrogen bonds : angle 5.70431 ( 1668) link_ALPHA1-2 : bond 0.00245 ( 4) link_ALPHA1-2 : angle 2.57377 ( 12) link_ALPHA1-3 : bond 0.00581 ( 8) link_ALPHA1-3 : angle 2.08302 ( 24) link_ALPHA1-6 : bond 0.00377 ( 8) link_ALPHA1-6 : angle 1.46270 ( 24) link_BETA1-4 : bond 0.00491 ( 31) link_BETA1-4 : angle 1.67851 ( 93) link_BETA1-6 : bond 0.00729 ( 2) link_BETA1-6 : angle 1.06732 ( 6) link_NAG-ASN : bond 0.00373 ( 23) link_NAG-ASN : angle 2.34142 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7399.52 seconds wall clock time: 126 minutes 32.19 seconds (7592.19 seconds total)