Starting phenix.real_space_refine on Tue May 20 22:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3n_29705/05_2025/8g3n_29705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3n_29705/05_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_29705/05_2025/8g3n_29705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3n_29705/05_2025/8g3n_29705.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3n_29705/05_2025/8g3n_29705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3n_29705/05_2025/8g3n_29705.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 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: 13.15, per 1000 atoms: 0.65 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: 5.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 2.82 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: 7.13 Time building geometry restraints manager: 6.57 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 469 or resid 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.380 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (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 TRP 0.113 0.014 TRP J 115 HIS 0.032 0.005 HIS L 168 PHE 0.062 0.012 PHE L 205 TYR 0.058 0.012 TYR J 121 ARG 0.022 0.004 ARG L 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 23) link_NAG-ASN : angle 5.33814 ( 69) 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_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) hydrogen bonds : bond 0.14918 ( 624) hydrogen bonds : angle 8.16693 ( 1668) link_BETA1-6 : bond 0.01864 ( 2) link_BETA1-6 : angle 4.41534 ( 6) SS BOND : bond 0.08872 ( 44) SS BOND : angle 2.97254 ( 88) covalent geometry : bond 0.01636 (20756) covalent geometry : angle 1.75532 (28182) *********************** 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 : 2.034 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: 0.8461 (tp) REVERT: A 10 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8290 (tp30) REVERT: A 13 GLU cc_start: 0.9044 (mp0) cc_final: 0.8835 (pm20) 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: 0.8458 (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: 0.8461 (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: 0.8461 (tp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 1.6577 time to fit residues: 503.5412 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 : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.092118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060326 restraints weight = 39259.318| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.92 r_work: 0.2785 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20876 Z= 0.152 Angle : 0.714 8.202 28498 Z= 0.364 Chirality : 0.047 0.168 3292 Planarity : 0.004 0.056 3534 Dihedral : 9.834 71.748 4264 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 2.38 % Allowed : 9.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2488 helix: -0.22 (0.97), residues: 24 sheet: 0.21 (0.15), residues: 1100 loop : -0.70 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 178 HIS 0.004 0.001 HIS G 347 PHE 0.013 0.002 PHE J 410 TYR 0.013 0.002 TYR F 49 ARG 0.007 0.001 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 23) link_NAG-ASN : angle 2.73694 ( 69) link_ALPHA1-6 : bond 0.00560 ( 8) link_ALPHA1-6 : angle 1.16603 ( 24) link_BETA1-4 : bond 0.00544 ( 31) link_BETA1-4 : angle 2.27238 ( 93) link_ALPHA1-2 : bond 0.00573 ( 4) link_ALPHA1-2 : angle 2.02978 ( 12) link_ALPHA1-3 : bond 0.00959 ( 8) link_ALPHA1-3 : angle 2.23370 ( 24) hydrogen bonds : bond 0.04035 ( 624) hydrogen bonds : angle 6.57703 ( 1668) link_BETA1-6 : bond 0.01908 ( 2) link_BETA1-6 : angle 1.42764 ( 6) SS BOND : bond 0.00427 ( 44) SS BOND : angle 1.03681 ( 88) covalent geometry : bond 0.00334 (20756) covalent geometry : angle 0.68513 (28182) *********************** 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 283 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 2.128 Fit side-chains revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8332 (mp0) REVERT: E 23 LYS cc_start: 0.8654 (tttp) cc_final: 0.8294 (tttp) REVERT: E 65 GLN cc_start: 0.8259 (tt0) cc_final: 0.7615 (mt0) REVERT: E 73 ASP cc_start: 0.7205 (t0) cc_final: 0.6637 (t0) REVERT: F 61 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: F 70 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7453 (mm-30) REVERT: F 79 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7722 (mp-120) REVERT: F 81 GLU cc_start: 0.8466 (pm20) cc_final: 0.8266 (pm20) REVERT: F 82 ASP cc_start: 0.8414 (m-30) cc_final: 0.7189 (m-30) REVERT: F 106 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5960 (tm-30) REVERT: A 10 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8248 (tp30) REVERT: A 23 LYS cc_start: 0.8678 (tttp) cc_final: 0.8332 (tttp) REVERT: A 65 GLN cc_start: 0.8313 (tt0) cc_final: 0.7735 (mt0) REVERT: A 73 ASP cc_start: 0.7215 (t0) cc_final: 0.6652 (t0) REVERT: D 61 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7530 (ptm160) REVERT: D 70 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7451 (mm-30) REVERT: D 79 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7722 (mp-120) REVERT: D 81 GLU cc_start: 0.8463 (pm20) cc_final: 0.8259 (pm20) REVERT: D 82 ASP cc_start: 0.8450 (m-30) cc_final: 0.7170 (m-30) REVERT: B 10 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8321 (mp0) REVERT: B 23 LYS cc_start: 0.8663 (tttp) cc_final: 0.8304 (tttp) REVERT: B 65 GLN cc_start: 0.8251 (tt0) cc_final: 0.7635 (mt0) REVERT: B 73 ASP cc_start: 0.7170 (t0) cc_final: 0.6603 (t0) REVERT: H 61 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7421 (ptm160) REVERT: H 70 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7418 (mm-30) REVERT: H 79 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7727 (mp-120) REVERT: H 82 ASP cc_start: 0.8409 (m-30) cc_final: 0.7194 (m-30) REVERT: C 10 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8337 (mp0) REVERT: C 23 LYS cc_start: 0.8652 (tttp) cc_final: 0.8291 (tttp) REVERT: C 65 GLN cc_start: 0.8250 (tt0) cc_final: 0.7638 (mt0) REVERT: C 73 ASP cc_start: 0.7197 (t0) cc_final: 0.6631 (t0) REVERT: I 61 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7425 (ptm160) REVERT: I 70 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7418 (mm-30) REVERT: I 79 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7717 (mp-120) REVERT: I 82 ASP cc_start: 0.8431 (m-30) cc_final: 0.7153 (m-30) outliers start: 51 outliers final: 4 residues processed: 256 average time/residue: 1.6031 time to fit residues: 455.0595 Evaluate side-chains 203 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 41 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 136 GLN E 39 GLN F 93 ASN J 136 GLN A 39 GLN D 93 ASN B 39 GLN H 93 ASN L 136 GLN C 39 GLN I 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.055073 restraints weight = 40531.165| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.90 r_work: 0.2675 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.061 20876 Z= 0.457 Angle : 0.868 8.930 28498 Z= 0.439 Chirality : 0.056 0.160 3292 Planarity : 0.005 0.039 3534 Dihedral : 9.601 73.159 4264 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 9.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 2488 helix: -0.03 (1.18), residues: 24 sheet: 0.06 (0.15), residues: 1076 loop : -1.15 (0.14), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 178 HIS 0.011 0.003 HIS G 184 PHE 0.018 0.003 PHE K 410 TYR 0.027 0.003 TYR L 121 ARG 0.008 0.001 ARG E 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 23) link_NAG-ASN : angle 3.25100 ( 69) link_ALPHA1-6 : bond 0.00278 ( 8) link_ALPHA1-6 : angle 1.63998 ( 24) link_BETA1-4 : bond 0.00468 ( 31) link_BETA1-4 : angle 2.52767 ( 93) link_ALPHA1-2 : bond 0.00023 ( 4) link_ALPHA1-2 : angle 2.85933 ( 12) link_ALPHA1-3 : bond 0.00151 ( 8) link_ALPHA1-3 : angle 2.67421 ( 24) hydrogen bonds : bond 0.05072 ( 624) hydrogen bonds : angle 6.37718 ( 1668) link_BETA1-6 : bond 0.01121 ( 2) link_BETA1-6 : angle 1.06396 ( 6) SS BOND : bond 0.00583 ( 44) SS BOND : angle 1.66969 ( 88) covalent geometry : bond 0.01109 (20756) covalent geometry : angle 0.83291 (28182) *********************** 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 280 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8438 (mp0) REVERT: E 23 LYS cc_start: 0.8690 (tttp) cc_final: 0.7885 (tttp) REVERT: E 48 MET cc_start: 0.9241 (mtp) cc_final: 0.9004 (mtm) REVERT: E 65 GLN cc_start: 0.8593 (tt0) cc_final: 0.7965 (mt0) REVERT: E 73 ASP cc_start: 0.7367 (t0) cc_final: 0.6855 (t0) REVERT: E 77 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7911 (p) REVERT: E 107 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8848 (m-30) REVERT: F 11 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8419 (tt) REVERT: F 79 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7665 (mp-120) REVERT: F 82 ASP cc_start: 0.8519 (m-30) cc_final: 0.7332 (m-30) REVERT: A 10 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8408 (tp30) REVERT: A 23 LYS cc_start: 0.8702 (tttp) cc_final: 0.8109 (tttp) REVERT: A 65 GLN cc_start: 0.8609 (tt0) cc_final: 0.8024 (mt0) REVERT: A 73 ASP cc_start: 0.7357 (t0) cc_final: 0.6850 (t0) REVERT: D 11 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8421 (tt) REVERT: D 79 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7665 (mp-120) REVERT: D 82 ASP cc_start: 0.8528 (m-30) cc_final: 0.7367 (m-30) REVERT: B 10 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8418 (mp0) REVERT: B 23 LYS cc_start: 0.8698 (tttp) cc_final: 0.7894 (tttp) REVERT: B 65 GLN cc_start: 0.8591 (tt0) cc_final: 0.7962 (mt0) REVERT: B 73 ASP cc_start: 0.7335 (t0) cc_final: 0.6826 (t0) REVERT: B 77 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 107 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8845 (m-30) REVERT: H 11 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 10 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8451 (mp0) REVERT: C 23 LYS cc_start: 0.8690 (tttp) cc_final: 0.7882 (tttp) REVERT: C 65 GLN cc_start: 0.8591 (tt0) cc_final: 0.7966 (mt0) REVERT: C 73 ASP cc_start: 0.7345 (t0) cc_final: 0.6836 (t0) REVERT: C 77 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (p) REVERT: C 107 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: I 11 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8416 (tt) outliers start: 80 outliers final: 17 residues processed: 249 average time/residue: 1.5921 time to fit residues: 440.2793 Evaluate side-chains 217 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 MET 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 11 LEU 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 215 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 11 LEU 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 215 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain H residue 11 LEU 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 C residue 77 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain I residue 11 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 91 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 402 ASN E 39 GLN F 6 GLN A 39 GLN D 6 GLN B 39 GLN H 6 GLN C 39 GLN I 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058288 restraints weight = 40087.661| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.93 r_work: 0.2746 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20876 Z= 0.135 Angle : 0.655 8.823 28498 Z= 0.326 Chirality : 0.046 0.162 3292 Planarity : 0.004 0.047 3534 Dihedral : 7.857 60.421 4264 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.99 % Rotamer: Outliers : 2.80 % Allowed : 10.89 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2488 helix: -0.23 (1.06), residues: 24 sheet: 0.31 (0.15), residues: 1072 loop : -0.99 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 178 HIS 0.002 0.001 HIS L 347 PHE 0.013 0.002 PHE J 410 TYR 0.013 0.001 TYR L 121 ARG 0.009 0.001 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 23) link_NAG-ASN : angle 2.31390 ( 69) link_ALPHA1-6 : bond 0.00554 ( 8) link_ALPHA1-6 : angle 1.32263 ( 24) link_BETA1-4 : bond 0.00551 ( 31) link_BETA1-4 : angle 1.78477 ( 93) link_ALPHA1-2 : bond 0.00512 ( 4) link_ALPHA1-2 : angle 2.44132 ( 12) link_ALPHA1-3 : bond 0.00979 ( 8) link_ALPHA1-3 : angle 1.75924 ( 24) hydrogen bonds : bond 0.03634 ( 624) hydrogen bonds : angle 6.03189 ( 1668) link_BETA1-6 : bond 0.00895 ( 2) link_BETA1-6 : angle 1.06831 ( 6) SS BOND : bond 0.00270 ( 44) SS BOND : angle 0.93216 ( 88) covalent geometry : bond 0.00310 (20756) covalent geometry : angle 0.63316 (28182) *********************** 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 283 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 2.338 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: 0.9001 (mm-30) cc_final: 0.8457 (mp0) REVERT: E 23 LYS cc_start: 0.8698 (tttp) cc_final: 0.8181 (tttp) REVERT: E 46 GLU cc_start: 0.8562 (tt0) cc_final: 0.8290 (tt0) REVERT: E 48 MET cc_start: 0.9242 (mtp) cc_final: 0.8991 (mtm) REVERT: E 65 GLN cc_start: 0.8415 (tt0) cc_final: 0.7834 (mm-40) REVERT: E 73 ASP cc_start: 0.7333 (t0) cc_final: 0.6726 (t0) REVERT: F 11 LEU cc_start: 0.8639 (tp) cc_final: 0.8364 (tt) REVERT: F 82 ASP cc_start: 0.8554 (m-30) cc_final: 0.8277 (m-30) REVERT: A 10 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8459 (tp30) REVERT: A 23 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8635 (tptt) REVERT: A 65 GLN cc_start: 0.8386 (tt0) cc_final: 0.7730 (mm-40) REVERT: A 73 ASP cc_start: 0.7350 (t0) cc_final: 0.6723 (t0) REVERT: A 77 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 87 ARG cc_start: 0.7547 (mtm110) cc_final: 0.6852 (ptp-110) REVERT: A 90 ASP cc_start: 0.7982 (m-30) cc_final: 0.7748 (m-30) REVERT: D 11 LEU cc_start: 0.8721 (tp) cc_final: 0.8434 (tt) REVERT: D 82 ASP cc_start: 0.8547 (m-30) cc_final: 0.8302 (m-30) REVERT: B 10 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8446 (mp0) REVERT: B 23 LYS cc_start: 0.8708 (tttp) cc_final: 0.8196 (tttp) REVERT: B 46 GLU cc_start: 0.8677 (tt0) cc_final: 0.8405 (tt0) REVERT: B 65 GLN cc_start: 0.8343 (tt0) cc_final: 0.7688 (mm-40) REVERT: B 73 ASP cc_start: 0.7328 (t0) cc_final: 0.6723 (t0) REVERT: H 4 MET cc_start: 0.7757 (mmp) cc_final: 0.7551 (mmp) REVERT: H 11 LEU cc_start: 0.8733 (tp) cc_final: 0.8452 (tt) REVERT: H 82 ASP cc_start: 0.8439 (m-30) cc_final: 0.8189 (m-30) REVERT: C 10 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8466 (mp0) REVERT: C 23 LYS cc_start: 0.8699 (tttp) cc_final: 0.8182 (tttp) REVERT: C 46 GLU cc_start: 0.8675 (tt0) cc_final: 0.8400 (tt0) REVERT: C 65 GLN cc_start: 0.8338 (tt0) cc_final: 0.7764 (mm-40) REVERT: C 73 ASP cc_start: 0.7329 (t0) cc_final: 0.6723 (t0) REVERT: I 4 MET cc_start: 0.7738 (mmp) cc_final: 0.7534 (mmp) REVERT: I 11 LEU cc_start: 0.8650 (tp) cc_final: 0.8368 (tt) outliers start: 60 outliers final: 15 residues processed: 258 average time/residue: 1.6690 time to fit residues: 475.6311 Evaluate side-chains 226 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 467 MET Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 47 LEU 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 L residue 467 MET Chi-restraints excluded: chain C residue 35 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN A 39 GLN D 6 GLN H 6 GLN I 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057090 restraints weight = 40329.601| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.93 r_work: 0.2716 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 20876 Z= 0.213 Angle : 0.702 9.829 28498 Z= 0.349 Chirality : 0.047 0.179 3292 Planarity : 0.005 0.048 3534 Dihedral : 7.596 59.650 4264 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 2.80 % Allowed : 11.59 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2488 helix: -0.19 (1.10), residues: 24 sheet: 0.37 (0.16), residues: 1064 loop : -1.00 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 178 HIS 0.006 0.002 HIS K 184 PHE 0.015 0.002 PHE J 410 TYR 0.018 0.002 TYR L 121 ARG 0.011 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 23) link_NAG-ASN : angle 2.53348 ( 69) link_ALPHA1-6 : bond 0.00441 ( 8) link_ALPHA1-6 : angle 1.43879 ( 24) link_BETA1-4 : bond 0.00488 ( 31) link_BETA1-4 : angle 1.86970 ( 93) link_ALPHA1-2 : bond 0.00257 ( 4) link_ALPHA1-2 : angle 2.54924 ( 12) link_ALPHA1-3 : bond 0.00591 ( 8) link_ALPHA1-3 : angle 2.11152 ( 24) hydrogen bonds : bond 0.03846 ( 624) hydrogen bonds : angle 5.96727 ( 1668) link_BETA1-6 : bond 0.00912 ( 2) link_BETA1-6 : angle 1.05562 ( 6) SS BOND : bond 0.00295 ( 44) SS BOND : angle 1.14690 ( 88) covalent geometry : bond 0.00508 (20756) covalent geometry : angle 0.67658 (28182) *********************** 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 280 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 2.080 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: E 10 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8507 (mp0) REVERT: E 23 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8605 (tptt) REVERT: E 39 GLN cc_start: 0.7590 (tt0) cc_final: 0.6929 (tp40) REVERT: E 46 GLU cc_start: 0.8657 (tt0) cc_final: 0.8113 (tt0) REVERT: E 63 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8699 (mtm110) REVERT: E 65 GLN cc_start: 0.8473 (tt0) cc_final: 0.7884 (mm-40) REVERT: E 73 ASP cc_start: 0.7398 (t0) cc_final: 0.6770 (t0) REVERT: E 77 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7816 (p) REVERT: F 11 LEU cc_start: 0.8690 (tp) cc_final: 0.8435 (tt) REVERT: F 81 GLU cc_start: 0.8580 (pm20) cc_final: 0.8369 (pm20) REVERT: F 82 ASP cc_start: 0.8616 (m-30) cc_final: 0.8219 (m-30) REVERT: F 104 LYS cc_start: 0.8202 (tppt) cc_final: 0.7997 (tppt) REVERT: A 10 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8452 (tp30) REVERT: A 23 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8660 (tttp) REVERT: A 39 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: A 46 GLU cc_start: 0.8712 (tt0) cc_final: 0.8161 (tt0) REVERT: A 65 GLN cc_start: 0.8457 (tt0) cc_final: 0.7893 (mm-40) REVERT: A 73 ASP cc_start: 0.7407 (t0) cc_final: 0.6790 (t0) REVERT: A 77 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 90 ASP cc_start: 0.7842 (m-30) cc_final: 0.7499 (m-30) REVERT: D 11 LEU cc_start: 0.8683 (tp) cc_final: 0.8414 (tt) REVERT: D 82 ASP cc_start: 0.8510 (m-30) cc_final: 0.8220 (m-30) REVERT: B 10 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8499 (mp0) REVERT: B 23 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8615 (tptt) REVERT: B 39 GLN cc_start: 0.7608 (tt0) cc_final: 0.6934 (tp40) REVERT: B 46 GLU cc_start: 0.8653 (tt0) cc_final: 0.8206 (tt0) REVERT: B 65 GLN cc_start: 0.8446 (tt0) cc_final: 0.7829 (mm-40) REVERT: B 73 ASP cc_start: 0.7383 (t0) cc_final: 0.6757 (t0) REVERT: B 77 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7821 (p) REVERT: H 11 LEU cc_start: 0.8739 (tp) cc_final: 0.8473 (tt) REVERT: H 81 GLU cc_start: 0.8476 (pm20) cc_final: 0.8269 (pm20) REVERT: H 82 ASP cc_start: 0.8480 (m-30) cc_final: 0.8113 (m-30) REVERT: H 104 LYS cc_start: 0.8390 (tppt) cc_final: 0.8177 (tppt) REVERT: C 10 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8510 (mp0) REVERT: C 23 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8614 (tptt) REVERT: C 39 GLN cc_start: 0.7599 (tt0) cc_final: 0.6927 (tp40) REVERT: C 46 GLU cc_start: 0.8655 (tt0) cc_final: 0.8127 (tt0) REVERT: C 65 GLN cc_start: 0.8456 (tt0) cc_final: 0.7853 (mm-40) REVERT: C 73 ASP cc_start: 0.7382 (t0) cc_final: 0.6756 (t0) REVERT: C 77 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7817 (p) REVERT: I 11 LEU cc_start: 0.8686 (tp) cc_final: 0.8428 (tt) REVERT: I 82 ASP cc_start: 0.8401 (m-30) cc_final: 0.8166 (m-30) REVERT: I 104 LYS cc_start: 0.8181 (tppt) cc_final: 0.7973 (tppt) outliers start: 60 outliers final: 18 residues processed: 254 average time/residue: 1.5464 time to fit residues: 438.2424 Evaluate side-chains 243 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 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 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 77 THR 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 23 LYS Chi-restraints excluded: chain B residue 77 THR 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 23 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 90 optimal weight: 0.3980 chunk 178 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 0.0570 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS F 6 GLN J 347 HIS D 6 GLN K 347 HIS H 6 GLN L 347 HIS I 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056798 restraints weight = 40380.903| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.95 r_work: 0.2709 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20876 Z= 0.229 Angle : 0.712 10.712 28498 Z= 0.352 Chirality : 0.047 0.181 3292 Planarity : 0.005 0.046 3534 Dihedral : 7.504 58.755 4264 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 2.94 % Allowed : 12.80 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2488 helix: -0.22 (1.10), residues: 24 sheet: 0.33 (0.16), residues: 1048 loop : -1.01 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 178 HIS 0.005 0.001 HIS J 347 PHE 0.015 0.002 PHE G 410 TYR 0.017 0.001 TYR L 121 ARG 0.011 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 23) link_NAG-ASN : angle 2.49447 ( 69) link_ALPHA1-6 : bond 0.00408 ( 8) link_ALPHA1-6 : angle 1.43882 ( 24) link_BETA1-4 : bond 0.00485 ( 31) link_BETA1-4 : angle 1.79806 ( 93) link_ALPHA1-2 : bond 0.00251 ( 4) link_ALPHA1-2 : angle 2.62678 ( 12) link_ALPHA1-3 : bond 0.00579 ( 8) link_ALPHA1-3 : angle 2.12709 ( 24) hydrogen bonds : bond 0.03873 ( 624) hydrogen bonds : angle 5.90848 ( 1668) link_BETA1-6 : bond 0.00860 ( 2) link_BETA1-6 : angle 1.03413 ( 6) SS BOND : bond 0.00299 ( 44) SS BOND : angle 1.03288 ( 88) covalent geometry : bond 0.00548 (20756) covalent geometry : angle 0.68840 (28182) *********************** 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 281 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 2.166 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 128 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (ptmt) REVERT: E 10 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8497 (mp0) REVERT: E 23 LYS cc_start: 0.8879 (tttp) cc_final: 0.8634 (tttp) REVERT: E 46 GLU cc_start: 0.8676 (tt0) cc_final: 0.8193 (tt0) REVERT: E 65 GLN cc_start: 0.8502 (tt0) cc_final: 0.7920 (mm-40) REVERT: E 73 ASP cc_start: 0.7403 (t0) cc_final: 0.6789 (t0) REVERT: E 77 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7934 (p) REVERT: F 11 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8399 (tt) REVERT: F 82 ASP cc_start: 0.8457 (m-30) cc_final: 0.8076 (m-30) REVERT: J 128 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8189 (ptmt) REVERT: A 10 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8443 (tp30) REVERT: A 23 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8529 (tttp) REVERT: A 46 GLU cc_start: 0.8618 (tt0) cc_final: 0.8210 (tt0) REVERT: A 65 GLN cc_start: 0.8474 (tt0) cc_final: 0.7915 (mm-40) REVERT: A 73 ASP cc_start: 0.7436 (t0) cc_final: 0.6809 (t0) REVERT: A 77 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7904 (p) REVERT: A 87 ARG cc_start: 0.7545 (ptp-110) cc_final: 0.7069 (ptp-170) REVERT: D 11 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8397 (tt) REVERT: D 24 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7917 (ptm160) REVERT: K 128 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: B 10 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8485 (mp0) REVERT: B 23 LYS cc_start: 0.8888 (tttp) cc_final: 0.8671 (tttp) REVERT: B 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8090 (tt0) REVERT: B 65 GLN cc_start: 0.8461 (tt0) cc_final: 0.7844 (mm-40) REVERT: B 73 ASP cc_start: 0.7403 (t0) cc_final: 0.6789 (t0) REVERT: B 77 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7944 (p) REVERT: H 11 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8405 (tt) REVERT: H 82 ASP cc_start: 0.8389 (m-30) cc_final: 0.8044 (m-30) REVERT: L 128 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8200 (ptmt) REVERT: C 10 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8502 (mp0) REVERT: C 23 LYS cc_start: 0.8884 (tttp) cc_final: 0.8665 (tttp) REVERT: C 46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8132 (tt0) REVERT: C 65 GLN cc_start: 0.8456 (tt0) cc_final: 0.7861 (mm-40) REVERT: C 73 ASP cc_start: 0.7397 (t0) cc_final: 0.6784 (t0) REVERT: C 77 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7934 (p) REVERT: I 11 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8386 (tt) REVERT: I 82 ASP cc_start: 0.8409 (m-30) cc_final: 0.8122 (m-30) outliers start: 63 outliers final: 27 residues processed: 256 average time/residue: 1.5870 time to fit residues: 450.8010 Evaluate side-chains 257 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 128 LYS 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 77 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 128 LYS 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 77 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 128 LYS 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 77 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 128 LYS 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 77 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN F 32 ASN F 92 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 32 ASN D 92 ASN H 6 GLN H 32 ASN H 92 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 32 ASN I 92 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058291 restraints weight = 39941.245| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.92 r_work: 0.2744 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20876 Z= 0.141 Angle : 0.673 11.224 28498 Z= 0.331 Chirality : 0.045 0.187 3292 Planarity : 0.005 0.067 3534 Dihedral : 6.908 52.626 4264 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 13.74 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2488 helix: -0.27 (1.05), residues: 24 sheet: 0.37 (0.16), residues: 1060 loop : -0.94 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 178 HIS 0.003 0.001 HIS L 184 PHE 0.013 0.002 PHE L 422 TYR 0.020 0.001 TYR I 49 ARG 0.013 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 23) link_NAG-ASN : angle 2.19531 ( 69) link_ALPHA1-6 : bond 0.00521 ( 8) link_ALPHA1-6 : angle 1.38206 ( 24) link_BETA1-4 : bond 0.00536 ( 31) link_BETA1-4 : angle 1.54980 ( 93) link_ALPHA1-2 : bond 0.00420 ( 4) link_ALPHA1-2 : angle 2.46845 ( 12) link_ALPHA1-3 : bond 0.00874 ( 8) link_ALPHA1-3 : angle 1.81342 ( 24) hydrogen bonds : bond 0.03382 ( 624) hydrogen bonds : angle 5.68489 ( 1668) link_BETA1-6 : bond 0.00767 ( 2) link_BETA1-6 : angle 1.09740 ( 6) SS BOND : bond 0.00244 ( 44) SS BOND : angle 0.78636 ( 88) covalent geometry : bond 0.00330 (20756) covalent geometry : angle 0.65511 (28182) *********************** 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 297 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 2.097 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: E 10 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8543 (mp0) REVERT: E 23 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8560 (tttp) REVERT: E 46 GLU cc_start: 0.8652 (tt0) cc_final: 0.8068 (tt0) REVERT: E 65 GLN cc_start: 0.8443 (tt0) cc_final: 0.7793 (mm-40) REVERT: E 73 ASP cc_start: 0.7430 (t0) cc_final: 0.6804 (t0) REVERT: E 77 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7924 (p) REVERT: E 87 ARG cc_start: 0.7392 (mtm110) cc_final: 0.6780 (ptp-110) REVERT: E 90 ASP cc_start: 0.8102 (m-30) cc_final: 0.7784 (m-30) REVERT: F 6 GLN cc_start: 0.7699 (tt0) cc_final: 0.7193 (tt0) REVERT: F 11 LEU cc_start: 0.8686 (tp) cc_final: 0.8411 (tt) REVERT: A 10 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8417 (tp30) REVERT: A 46 GLU cc_start: 0.8628 (tt0) cc_final: 0.7975 (tt0) REVERT: A 65 GLN cc_start: 0.8435 (tt0) cc_final: 0.7879 (mm-40) REVERT: A 73 ASP cc_start: 0.7461 (t0) cc_final: 0.6844 (t0) REVERT: A 77 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 87 ARG cc_start: 0.7581 (ptp-110) cc_final: 0.6949 (ptp-170) REVERT: D 6 GLN cc_start: 0.7829 (tt0) cc_final: 0.7442 (tt0) REVERT: D 11 LEU cc_start: 0.8674 (tp) cc_final: 0.8416 (tt) REVERT: D 82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7784 (m-30) REVERT: B 10 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8537 (mp0) REVERT: B 23 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8567 (tttp) REVERT: B 46 GLU cc_start: 0.8604 (tt0) cc_final: 0.8092 (tt0) REVERT: B 65 GLN cc_start: 0.8492 (tt0) cc_final: 0.7888 (mm-40) REVERT: B 73 ASP cc_start: 0.7432 (t0) cc_final: 0.6803 (t0) REVERT: B 77 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7926 (p) REVERT: B 87 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6809 (ptp-110) REVERT: B 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7777 (m-30) REVERT: H 6 GLN cc_start: 0.7849 (tt0) cc_final: 0.7373 (tt0) REVERT: H 11 LEU cc_start: 0.8709 (tp) cc_final: 0.8442 (tt) REVERT: H 82 ASP cc_start: 0.8173 (m-30) cc_final: 0.7794 (m-30) REVERT: C 10 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8551 (mp0) REVERT: C 23 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8562 (tttp) REVERT: C 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.8048 (tt0) REVERT: C 65 GLN cc_start: 0.8442 (tt0) cc_final: 0.7753 (mm-40) REVERT: C 73 ASP cc_start: 0.7420 (t0) cc_final: 0.6796 (t0) REVERT: C 77 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7923 (p) REVERT: C 87 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6781 (ptp-110) REVERT: C 90 ASP cc_start: 0.8108 (m-30) cc_final: 0.7779 (m-30) REVERT: I 6 GLN cc_start: 0.7840 (tt0) cc_final: 0.7359 (tt0) REVERT: I 11 LEU cc_start: 0.8674 (tp) cc_final: 0.8404 (tt) REVERT: I 82 ASP cc_start: 0.7908 (m-30) cc_final: 0.7428 (m-30) outliers start: 61 outliers final: 21 residues processed: 274 average time/residue: 1.5498 time to fit residues: 471.8273 Evaluate side-chains 244 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL 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 51 ILE Chi-restraints excluded: chain E residue 77 THR 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 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 LYS 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 H residue 61 ARG Chi-restraints excluded: chain L residue 215 VAL 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 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 441 ASN K 441 ASN L 441 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.058293 restraints weight = 40285.660| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.95 r_work: 0.2744 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20876 Z= 0.147 Angle : 0.683 11.284 28498 Z= 0.333 Chirality : 0.046 0.187 3292 Planarity : 0.004 0.052 3534 Dihedral : 6.710 50.378 4264 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 1.92 % Allowed : 14.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2488 helix: -0.29 (1.04), residues: 24 sheet: 0.38 (0.16), residues: 1068 loop : -0.94 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 178 HIS 0.004 0.001 HIS G 184 PHE 0.013 0.002 PHE L 422 TYR 0.013 0.001 TYR L 121 ARG 0.013 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 23) link_NAG-ASN : angle 2.16876 ( 69) link_ALPHA1-6 : bond 0.00504 ( 8) link_ALPHA1-6 : angle 1.40815 ( 24) link_BETA1-4 : bond 0.00530 ( 31) link_BETA1-4 : angle 1.53697 ( 93) link_ALPHA1-2 : bond 0.00440 ( 4) link_ALPHA1-2 : angle 2.45865 ( 12) link_ALPHA1-3 : bond 0.00774 ( 8) link_ALPHA1-3 : angle 1.85306 ( 24) hydrogen bonds : bond 0.03347 ( 624) hydrogen bonds : angle 5.63433 ( 1668) link_BETA1-6 : bond 0.00724 ( 2) link_BETA1-6 : angle 1.09202 ( 6) SS BOND : bond 0.00267 ( 44) SS BOND : angle 1.09516 ( 88) covalent geometry : bond 0.00348 (20756) covalent geometry : angle 0.66387 (28182) *********************** 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 265 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 2.437 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: 0.9090 (mm-30) cc_final: 0.8532 (mp0) REVERT: E 46 GLU cc_start: 0.8704 (tt0) cc_final: 0.8200 (tt0) REVERT: E 65 GLN cc_start: 0.8334 (tt0) cc_final: 0.7746 (mm-40) REVERT: E 73 ASP cc_start: 0.7411 (t0) cc_final: 0.6792 (t0) REVERT: E 98 ARG cc_start: 0.8848 (ptp-110) cc_final: 0.8556 (ptm160) REVERT: F 11 LEU cc_start: 0.8678 (tp) cc_final: 0.8417 (tt) REVERT: F 78 LEU cc_start: 0.8466 (mm) cc_final: 0.8221 (mm) REVERT: A 10 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8446 (tp30) REVERT: A 23 LYS cc_start: 0.8867 (tttp) cc_final: 0.8589 (tttp) REVERT: A 46 GLU cc_start: 0.8651 (tt0) cc_final: 0.8161 (tt0) REVERT: A 65 GLN cc_start: 0.8355 (tt0) cc_final: 0.7822 (mm-40) REVERT: A 73 ASP cc_start: 0.7456 (t0) cc_final: 0.6863 (t0) REVERT: A 77 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 87 ARG cc_start: 0.7482 (ptp-110) cc_final: 0.7030 (ptp-170) REVERT: D 4 MET cc_start: 0.7745 (tpp) cc_final: 0.7452 (mmm) REVERT: D 6 GLN cc_start: 0.7650 (tt0) cc_final: 0.7278 (tt0) REVERT: D 11 LEU cc_start: 0.8665 (tp) cc_final: 0.8410 (tt) REVERT: D 78 LEU cc_start: 0.8480 (mm) cc_final: 0.8265 (mm) REVERT: B 10 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8523 (mp0) REVERT: B 46 GLU cc_start: 0.8711 (tt0) cc_final: 0.8172 (tt0) REVERT: B 65 GLN cc_start: 0.8472 (tt0) cc_final: 0.7878 (mm-40) REVERT: B 73 ASP cc_start: 0.7412 (t0) cc_final: 0.6788 (t0) REVERT: B 98 ARG cc_start: 0.8850 (ptp-110) cc_final: 0.8557 (ptm160) REVERT: H 11 LEU cc_start: 0.8698 (tp) cc_final: 0.8447 (tt) REVERT: H 82 ASP cc_start: 0.8174 (m-30) cc_final: 0.7766 (m-30) REVERT: C 10 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8539 (mp0) REVERT: C 46 GLU cc_start: 0.8679 (tt0) cc_final: 0.8194 (tt0) REVERT: C 65 GLN cc_start: 0.8369 (tt0) cc_final: 0.7771 (mm-40) REVERT: C 73 ASP cc_start: 0.7401 (t0) cc_final: 0.6778 (t0) REVERT: C 98 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8557 (ptm160) REVERT: I 11 LEU cc_start: 0.8679 (tp) cc_final: 0.8402 (tt) REVERT: I 82 ASP cc_start: 0.7750 (m-30) cc_final: 0.7506 (m-30) outliers start: 41 outliers final: 30 residues processed: 251 average time/residue: 1.6212 time to fit residues: 457.5390 Evaluate side-chains 239 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU 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 A residue 77 THR 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 390 LEU 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 H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 226 optimal weight: 8.9990 chunk 159 optimal weight: 0.0770 chunk 203 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057668 restraints weight = 40253.011| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.94 r_work: 0.2727 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20876 Z= 0.190 Angle : 0.714 11.497 28498 Z= 0.349 Chirality : 0.046 0.190 3292 Planarity : 0.005 0.065 3534 Dihedral : 6.844 51.595 4264 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 14.95 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2488 helix: -0.28 (1.06), residues: 24 sheet: 0.33 (0.16), residues: 1068 loop : -1.03 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 178 HIS 0.003 0.001 HIS J 184 PHE 0.014 0.002 PHE K 410 TYR 0.021 0.001 TYR F 49 ARG 0.016 0.001 ARG C 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 23) link_NAG-ASN : angle 2.27684 ( 69) link_ALPHA1-6 : bond 0.00437 ( 8) link_ALPHA1-6 : angle 1.44253 ( 24) link_BETA1-4 : bond 0.00490 ( 31) link_BETA1-4 : angle 1.61319 ( 93) link_ALPHA1-2 : bond 0.00297 ( 4) link_ALPHA1-2 : angle 2.53526 ( 12) link_ALPHA1-3 : bond 0.00653 ( 8) link_ALPHA1-3 : angle 1.99543 ( 24) hydrogen bonds : bond 0.03575 ( 624) hydrogen bonds : angle 5.66495 ( 1668) link_BETA1-6 : bond 0.00718 ( 2) link_BETA1-6 : angle 1.06419 ( 6) SS BOND : bond 0.00320 ( 44) SS BOND : angle 1.10281 ( 88) covalent geometry : bond 0.00457 (20756) covalent geometry : angle 0.69423 (28182) *********************** 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 268 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 2.094 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: E 10 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8531 (mp0) REVERT: E 23 LYS cc_start: 0.8817 (tttp) cc_final: 0.8219 (tptp) REVERT: E 46 GLU cc_start: 0.8708 (tt0) cc_final: 0.8137 (tt0) REVERT: E 65 GLN cc_start: 0.8512 (tt0) cc_final: 0.7891 (mm-40) REVERT: E 73 ASP cc_start: 0.7479 (t0) cc_final: 0.6915 (t0) REVERT: E 77 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 10 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8433 (tp30) REVERT: A 23 LYS cc_start: 0.8906 (tttp) cc_final: 0.8582 (tttp) REVERT: A 46 GLU cc_start: 0.8741 (tt0) cc_final: 0.8079 (tt0) REVERT: A 65 GLN cc_start: 0.8465 (tt0) cc_final: 0.7936 (mm-40) REVERT: A 73 ASP cc_start: 0.7515 (t0) cc_final: 0.6901 (t0) REVERT: A 87 ARG cc_start: 0.7667 (ptp-110) cc_final: 0.7063 (ptp-170) REVERT: D 6 GLN cc_start: 0.7820 (tt0) cc_final: 0.7445 (tt0) REVERT: D 11 LEU cc_start: 0.8674 (tp) cc_final: 0.8427 (tt) REVERT: B 10 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8527 (mp0) REVERT: B 23 LYS cc_start: 0.8830 (tttp) cc_final: 0.8230 (tptp) REVERT: B 46 GLU cc_start: 0.8709 (tt0) cc_final: 0.8097 (tt0) REVERT: B 65 GLN cc_start: 0.8574 (tt0) cc_final: 0.8011 (mm-40) REVERT: B 73 ASP cc_start: 0.7485 (t0) cc_final: 0.6889 (t0) REVERT: B 77 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7839 (p) REVERT: H 11 LEU cc_start: 0.8659 (tp) cc_final: 0.8399 (tt) REVERT: H 82 ASP cc_start: 0.8099 (m-30) cc_final: 0.7868 (m-30) REVERT: C 10 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8534 (mp0) REVERT: C 23 LYS cc_start: 0.8828 (tttp) cc_final: 0.8225 (tptp) REVERT: C 46 GLU cc_start: 0.8690 (tt0) cc_final: 0.8082 (tt0) REVERT: C 65 GLN cc_start: 0.8453 (tt0) cc_final: 0.7824 (mm-40) REVERT: C 73 ASP cc_start: 0.7475 (t0) cc_final: 0.6883 (t0) REVERT: C 77 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (p) REVERT: I 18 ARG cc_start: 0.9124 (tpp80) cc_final: 0.8755 (tpp80) REVERT: I 82 ASP cc_start: 0.8007 (m-30) cc_final: 0.7787 (m-30) outliers start: 49 outliers final: 25 residues processed: 253 average time/residue: 1.4955 time to fit residues: 422.0766 Evaluate side-chains 237 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 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 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU 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 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 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 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 94 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN J 226 GLN J 441 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN K 441 ASN L 226 GLN L 441 ASN I 6 GLN I 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056310 restraints weight = 40181.565| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.93 r_work: 0.2700 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 20876 Z= 0.276 Angle : 0.779 11.689 28498 Z= 0.381 Chirality : 0.049 0.185 3292 Planarity : 0.005 0.055 3534 Dihedral : 7.420 57.794 4264 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 1.64 % Allowed : 16.17 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2488 helix: -0.29 (1.10), residues: 24 sheet: 0.26 (0.16), residues: 1068 loop : -1.18 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 178 HIS 0.004 0.001 HIS L 168 PHE 0.017 0.002 PHE G 410 TYR 0.022 0.002 TYR H 49 ARG 0.015 0.001 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 23) link_NAG-ASN : angle 2.55390 ( 69) link_ALPHA1-6 : bond 0.00298 ( 8) link_ALPHA1-6 : angle 1.50490 ( 24) link_BETA1-4 : bond 0.00471 ( 31) link_BETA1-4 : angle 1.82476 ( 93) link_ALPHA1-2 : bond 0.00147 ( 4) link_ALPHA1-2 : angle 2.68808 ( 12) link_ALPHA1-3 : bond 0.00424 ( 8) link_ALPHA1-3 : angle 2.30041 ( 24) hydrogen bonds : bond 0.04042 ( 624) hydrogen bonds : angle 5.82320 ( 1668) link_BETA1-6 : bond 0.00771 ( 2) link_BETA1-6 : angle 1.04486 ( 6) SS BOND : bond 0.00362 ( 44) SS BOND : angle 1.28187 ( 88) covalent geometry : bond 0.00664 (20756) covalent geometry : angle 0.75573 (28182) ********************** 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 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 2.139 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: E 10 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8550 (mp0) REVERT: E 23 LYS cc_start: 0.8822 (tttp) cc_final: 0.8222 (tptp) REVERT: E 46 GLU cc_start: 0.8774 (tt0) cc_final: 0.8320 (tt0) REVERT: E 65 GLN cc_start: 0.8614 (tt0) cc_final: 0.8033 (mm-40) REVERT: E 73 ASP cc_start: 0.7577 (t0) cc_final: 0.7020 (t0) REVERT: E 77 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (p) REVERT: F 4 MET cc_start: 0.7784 (tpp) cc_final: 0.7492 (mmm) REVERT: A 10 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8462 (tp30) REVERT: A 46 GLU cc_start: 0.8744 (tt0) cc_final: 0.8138 (tt0) REVERT: A 65 GLN cc_start: 0.8591 (tt0) cc_final: 0.8103 (mm-40) REVERT: A 73 ASP cc_start: 0.7601 (t0) cc_final: 0.7014 (t0) REVERT: A 87 ARG cc_start: 0.7472 (ptp-110) cc_final: 0.7017 (ptp-170) REVERT: D 18 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8765 (tpp80) REVERT: D 61 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8539 (ptm160) REVERT: B 10 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8537 (mp0) REVERT: B 23 LYS cc_start: 0.8833 (tttp) cc_final: 0.8463 (tttp) REVERT: B 46 GLU cc_start: 0.8762 (tt0) cc_final: 0.8268 (tt0) REVERT: B 65 GLN cc_start: 0.8659 (tt0) cc_final: 0.8121 (mm-40) REVERT: B 73 ASP cc_start: 0.7505 (t0) cc_final: 0.6947 (t0) REVERT: H 4 MET cc_start: 0.7803 (tpp) cc_final: 0.7522 (mmm) REVERT: H 18 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8908 (tpp80) REVERT: H 82 ASP cc_start: 0.8344 (m-30) cc_final: 0.8009 (m-30) REVERT: C 10 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8551 (mp0) REVERT: C 23 LYS cc_start: 0.8832 (tttp) cc_final: 0.8220 (tptp) REVERT: C 46 GLU cc_start: 0.8771 (tt0) cc_final: 0.8201 (tt0) REVERT: C 65 GLN cc_start: 0.8581 (tt0) cc_final: 0.8022 (mm-40) REVERT: C 73 ASP cc_start: 0.7520 (t0) cc_final: 0.6917 (t0) REVERT: C 77 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7898 (p) REVERT: I 4 MET cc_start: 0.7752 (tpp) cc_final: 0.7500 (mmm) REVERT: I 18 ARG cc_start: 0.9152 (tpp80) cc_final: 0.8841 (tpp80) REVERT: I 54 ARG cc_start: 0.8137 (pmm-80) cc_final: 0.7864 (ptp90) outliers start: 35 outliers final: 22 residues processed: 239 average time/residue: 1.5816 time to fit residues: 419.8535 Evaluate side-chains 236 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU 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 35 SER 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 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN J 226 GLN J 441 ASN K 226 GLN K 441 ASN L 226 GLN L 441 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058460 restraints weight = 40076.076| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.93 r_work: 0.2750 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20876 Z= 0.130 Angle : 0.694 11.941 28498 Z= 0.336 Chirality : 0.045 0.185 3292 Planarity : 0.005 0.072 3534 Dihedral : 6.677 49.987 4264 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 1.50 % Allowed : 16.40 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2488 helix: -0.42 (1.01), residues: 24 sheet: 0.35 (0.16), residues: 1068 loop : -1.03 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 178 HIS 0.002 0.001 HIS J 184 PHE 0.013 0.002 PHE J 422 TYR 0.022 0.001 TYR H 49 ARG 0.016 0.001 ARG B 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 23) link_NAG-ASN : angle 2.05932 ( 69) link_ALPHA1-6 : bond 0.00546 ( 8) link_ALPHA1-6 : angle 1.37601 ( 24) link_BETA1-4 : bond 0.00548 ( 31) link_BETA1-4 : angle 1.45620 ( 93) link_ALPHA1-2 : bond 0.00448 ( 4) link_ALPHA1-2 : angle 2.51652 ( 12) link_ALPHA1-3 : bond 0.00922 ( 8) link_ALPHA1-3 : angle 1.76475 ( 24) hydrogen bonds : bond 0.03258 ( 624) hydrogen bonds : angle 5.60384 ( 1668) link_BETA1-6 : bond 0.00674 ( 2) link_BETA1-6 : angle 1.09336 ( 6) SS BOND : bond 0.00243 ( 44) SS BOND : angle 0.96314 ( 88) covalent geometry : bond 0.00306 (20756) covalent geometry : angle 0.67751 (28182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17409.52 seconds wall clock time: 299 minutes 56.34 seconds (17996.34 seconds total)