Starting phenix.real_space_refine on Wed Jun 18 00:15:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3n_29705/06_2025/8g3n_29705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3n_29705/06_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_29705/06_2025/8g3n_29705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3n_29705/06_2025/8g3n_29705.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3n_29705/06_2025/8g3n_29705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3n_29705/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.56, per 1000 atoms: 0.67 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: 5.98 Conformation dependent library (CDL) restraints added in 2.8 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: 3.31 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: 7.99 Time building geometry restraints manager: 6.98 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: 3.780 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: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 51.060 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 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:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.850 ------------------------------------------------------------------------------- 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 : 2.190 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: 1.8807 time to fit residues: 570.1873 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 : 2.361 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060330 restraints weight = 39259.315| |-----------------------------------------------------------------------------| 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: 0.2646 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- 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 1.42763 ( 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 : 2.182 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: 0.8633 (tttp) cc_final: 0.8277 (tttp) REVERT: E 65 GLN cc_start: 0.8259 (tt0) cc_final: 0.7613 (mt0) REVERT: E 73 ASP cc_start: 0.7182 (t0) cc_final: 0.6620 (t0) REVERT: F 61 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7435 (ptm160) REVERT: F 70 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7444 (mm-30) REVERT: F 79 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7706 (mp-120) REVERT: F 82 ASP cc_start: 0.8390 (m-30) cc_final: 0.7168 (m-30) REVERT: F 106 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5950 (tm-30) REVERT: A 10 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8243 (tp30) REVERT: A 23 LYS cc_start: 0.8658 (tttp) cc_final: 0.8317 (tttp) REVERT: A 65 GLN cc_start: 0.8310 (tt0) cc_final: 0.7731 (mt0) REVERT: A 73 ASP cc_start: 0.7190 (t0) cc_final: 0.6633 (t0) REVERT: D 61 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7529 (ptm160) REVERT: D 70 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7442 (mm-30) REVERT: D 79 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7705 (mp-120) REVERT: D 81 GLU cc_start: 0.8461 (pm20) cc_final: 0.8255 (pm20) REVERT: D 82 ASP cc_start: 0.8429 (m-30) cc_final: 0.7151 (m-30) REVERT: B 10 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8320 (mp0) REVERT: B 23 LYS cc_start: 0.8642 (tttp) cc_final: 0.8288 (tttp) REVERT: B 65 GLN cc_start: 0.8251 (tt0) cc_final: 0.7632 (mt0) REVERT: B 73 ASP cc_start: 0.7141 (t0) cc_final: 0.6580 (t0) REVERT: H 61 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7414 (ptm160) REVERT: H 70 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7413 (mm-30) REVERT: H 79 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7712 (mp-120) REVERT: H 82 ASP cc_start: 0.8389 (m-30) cc_final: 0.7173 (m-30) REVERT: C 10 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8337 (mp0) REVERT: C 23 LYS cc_start: 0.8635 (tttp) cc_final: 0.8277 (tttp) REVERT: C 65 GLN cc_start: 0.8251 (tt0) cc_final: 0.7638 (mt0) REVERT: C 73 ASP cc_start: 0.7177 (t0) cc_final: 0.6616 (t0) REVERT: I 61 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7423 (ptm160) REVERT: I 70 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7410 (mm-30) REVERT: I 79 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7701 (mp-120) REVERT: I 81 GLU cc_start: 0.8458 (pm20) cc_final: 0.8258 (pm20) REVERT: I 82 ASP cc_start: 0.8410 (m-30) cc_final: 0.7132 (m-30) outliers start: 51 outliers final: 4 residues processed: 256 average time/residue: 1.7091 time to fit residues: 484.3132 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 : 2.365 ------------------------------------------------------------------------------- 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: 0.6980 chunk 118 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.086507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055160 restraints weight = 40547.634| |-----------------------------------------------------------------------------| 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: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.059 20876 Z= 0.445 Angle : 0.860 8.838 28498 Z= 0.436 Chirality : 0.056 0.160 3292 Planarity : 0.005 0.038 3534 Dihedral : 9.552 72.840 4264 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 3.32 % Allowed : 9.91 % Favored : 86.78 % 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: -0.88 (0.15), residues: 2488 helix: 0.05 (1.22), residues: 24 sheet: 0.08 (0.15), residues: 1076 loop : -1.14 (0.14), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 178 HIS 0.010 0.003 HIS J 184 PHE 0.018 0.003 PHE J 410 TYR 0.026 0.003 TYR J 121 ARG 0.008 0.001 ARG E 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 23) link_NAG-ASN : angle 3.22713 ( 69) link_ALPHA1-6 : bond 0.00263 ( 8) link_ALPHA1-6 : angle 1.65185 ( 24) link_BETA1-4 : bond 0.00486 ( 31) link_BETA1-4 : angle 2.52200 ( 93) link_ALPHA1-2 : bond 0.00043 ( 4) link_ALPHA1-2 : angle 2.89954 ( 12) link_ALPHA1-3 : bond 0.00171 ( 8) link_ALPHA1-3 : angle 2.64395 ( 24) hydrogen bonds : bond 0.05007 ( 624) hydrogen bonds : angle 6.37314 ( 1668) link_BETA1-6 : bond 0.01064 ( 2) link_BETA1-6 : angle 1.05154 ( 6) SS BOND : bond 0.00544 ( 44) SS BOND : angle 1.73790 ( 88) covalent geometry : bond 0.01078 (20756) covalent geometry : angle 0.82405 (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 271 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8438 (mp0) REVERT: E 23 LYS cc_start: 0.8689 (tttp) cc_final: 0.7886 (tttp) REVERT: E 48 MET cc_start: 0.9242 (mtp) cc_final: 0.9010 (mtm) REVERT: E 65 GLN cc_start: 0.8607 (tt0) cc_final: 0.7993 (mt0) REVERT: E 73 ASP cc_start: 0.7373 (t0) cc_final: 0.6863 (t0) REVERT: E 77 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (p) REVERT: E 107 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8850 (m-30) REVERT: F 11 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 10 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8411 (tp30) REVERT: A 23 LYS cc_start: 0.8705 (tttp) cc_final: 0.8117 (tttp) REVERT: A 65 GLN cc_start: 0.8616 (tt0) cc_final: 0.7990 (mm-40) REVERT: A 73 ASP cc_start: 0.7366 (t0) cc_final: 0.6861 (t0) REVERT: D 11 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8432 (tt) REVERT: D 79 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7663 (mp-120) REVERT: D 82 ASP cc_start: 0.8526 (m-30) cc_final: 0.7370 (m-30) REVERT: B 10 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8421 (mp0) REVERT: B 23 LYS cc_start: 0.8699 (tttp) cc_final: 0.7900 (tttp) REVERT: B 65 GLN cc_start: 0.8605 (tt0) cc_final: 0.7986 (mt0) REVERT: B 73 ASP cc_start: 0.7341 (t0) cc_final: 0.6832 (t0) REVERT: B 77 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7913 (p) REVERT: B 107 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8846 (m-30) REVERT: H 11 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8437 (tt) REVERT: C 10 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8451 (mp0) REVERT: C 23 LYS cc_start: 0.8689 (tttp) cc_final: 0.7885 (tttp) REVERT: C 65 GLN cc_start: 0.8604 (tt0) cc_final: 0.7990 (mt0) REVERT: C 73 ASP cc_start: 0.7349 (t0) cc_final: 0.6842 (t0) REVERT: C 77 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7911 (p) REVERT: C 107 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8841 (m-30) REVERT: I 11 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8425 (tt) REVERT: I 79 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7664 (mp-120) REVERT: I 82 ASP cc_start: 0.8508 (m-30) cc_final: 0.7358 (m-30) outliers start: 71 outliers final: 13 residues processed: 248 average time/residue: 1.9703 time to fit residues: 544.6833 Evaluate side-chains 215 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 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 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 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: 7.9990 chunk 173 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 225 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 B 39 GLN H 6 GLN C 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058762 restraints weight = 40020.815| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.91 r_work: 0.2757 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20876 Z= 0.119 Angle : 0.643 8.590 28498 Z= 0.321 Chirality : 0.045 0.167 3292 Planarity : 0.004 0.044 3534 Dihedral : 7.729 59.194 4264 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 3.08 % Allowed : 10.28 % 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: -0.55 (0.16), residues: 2488 helix: -0.23 (1.04), residues: 24 sheet: 0.36 (0.16), residues: 1072 loop : -0.96 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 178 HIS 0.002 0.001 HIS J 347 PHE 0.013 0.002 PHE L 410 TYR 0.010 0.001 TYR K 121 ARG 0.009 0.001 ARG A 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 23) link_NAG-ASN : angle 2.27746 ( 69) link_ALPHA1-6 : bond 0.00567 ( 8) link_ALPHA1-6 : angle 1.32982 ( 24) link_BETA1-4 : bond 0.00558 ( 31) link_BETA1-4 : angle 1.75050 ( 93) link_ALPHA1-2 : bond 0.00542 ( 4) link_ALPHA1-2 : angle 2.39294 ( 12) link_ALPHA1-3 : bond 0.00995 ( 8) link_ALPHA1-3 : angle 1.72676 ( 24) hydrogen bonds : bond 0.03548 ( 624) hydrogen bonds : angle 6.02029 ( 1668) link_BETA1-6 : bond 0.00975 ( 2) link_BETA1-6 : angle 1.08924 ( 6) SS BOND : bond 0.00237 ( 44) SS BOND : angle 0.90280 ( 88) covalent geometry : bond 0.00262 (20756) covalent geometry : angle 0.62130 (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 289 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 223 time to evaluate : 4.205 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: 0.9060 (mm-30) cc_final: 0.8482 (mp0) REVERT: E 23 LYS cc_start: 0.8700 (tttp) cc_final: 0.8192 (tttp) REVERT: E 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8265 (tt0) REVERT: E 48 MET cc_start: 0.9232 (mtp) cc_final: 0.8978 (mtm) REVERT: E 65 GLN cc_start: 0.8368 (tt0) cc_final: 0.7821 (mm-40) REVERT: E 73 ASP cc_start: 0.7325 (t0) cc_final: 0.6717 (t0) REVERT: E 107 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8948 (t70) REVERT: F 11 LEU cc_start: 0.8643 (tp) cc_final: 0.8361 (tt) REVERT: F 82 ASP cc_start: 0.8361 (m-30) cc_final: 0.8106 (m-30) REVERT: A 10 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8454 (tp30) REVERT: A 23 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8714 (tttp) REVERT: A 65 GLN cc_start: 0.8349 (tt0) cc_final: 0.7702 (mm-40) REVERT: A 73 ASP cc_start: 0.7338 (t0) cc_final: 0.6705 (t0) REVERT: A 77 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7821 (p) REVERT: A 87 ARG cc_start: 0.7545 (mtm110) cc_final: 0.6828 (ptp-110) REVERT: A 90 ASP cc_start: 0.7972 (m-30) cc_final: 0.7697 (m-30) REVERT: A 107 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8943 (t70) REVERT: D 11 LEU cc_start: 0.8694 (tp) cc_final: 0.8403 (tt) REVERT: D 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.8286 (m-30) REVERT: B 10 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8467 (mp0) REVERT: B 23 LYS cc_start: 0.8706 (tttp) cc_final: 0.8202 (tttp) REVERT: B 46 GLU cc_start: 0.8487 (tt0) cc_final: 0.8226 (tt0) REVERT: B 65 GLN cc_start: 0.8334 (tt0) cc_final: 0.7683 (mm-40) REVERT: B 73 ASP cc_start: 0.7313 (t0) cc_final: 0.6705 (t0) REVERT: B 107 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8962 (t70) REVERT: H 11 LEU cc_start: 0.8736 (tp) cc_final: 0.8450 (tt) REVERT: H 82 ASP cc_start: 0.8456 (m-30) cc_final: 0.8222 (m-30) REVERT: C 10 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8487 (mp0) REVERT: C 23 LYS cc_start: 0.8699 (tttp) cc_final: 0.8191 (tttp) REVERT: C 46 GLU cc_start: 0.8497 (tt0) cc_final: 0.8218 (tt0) REVERT: C 65 GLN cc_start: 0.8340 (tt0) cc_final: 0.7786 (mm-40) REVERT: C 73 ASP cc_start: 0.7317 (t0) cc_final: 0.6710 (t0) REVERT: C 107 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (t70) REVERT: I 11 LEU cc_start: 0.8650 (tp) cc_final: 0.8363 (tt) REVERT: I 82 ASP cc_start: 0.8507 (m-30) cc_final: 0.8241 (m-30) outliers start: 66 outliers final: 16 residues processed: 259 average time/residue: 2.2101 time to fit residues: 635.9077 Evaluate side-chains 231 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain 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 A residue 107 ASP 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 B residue 107 ASP Chi-restraints excluded: chain H residue 13 LEU 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 C residue 107 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN F 6 GLN J 441 ASN A 39 GLN D 6 GLN K 441 ASN H 6 GLN H 32 ASN H 92 ASN L 441 ASN I 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059368 restraints weight = 39937.366| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.93 r_work: 0.2769 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20876 Z= 0.119 Angle : 0.636 9.066 28498 Z= 0.315 Chirality : 0.045 0.183 3292 Planarity : 0.004 0.047 3534 Dihedral : 6.912 52.774 4264 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 2.76 % Allowed : 11.21 % Favored : 86.03 % 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: -0.36 (0.16), residues: 2488 helix: -0.26 (1.02), residues: 24 sheet: 0.41 (0.16), residues: 1084 loop : -0.76 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.003 0.001 HIS L 184 PHE 0.013 0.002 PHE J 354 TYR 0.018 0.001 TYR H 49 ARG 0.010 0.001 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 23) link_NAG-ASN : angle 2.17301 ( 69) link_ALPHA1-6 : bond 0.00602 ( 8) link_ALPHA1-6 : angle 1.38597 ( 24) link_BETA1-4 : bond 0.00540 ( 31) link_BETA1-4 : angle 1.59199 ( 93) link_ALPHA1-2 : bond 0.00505 ( 4) link_ALPHA1-2 : angle 2.30752 ( 12) link_ALPHA1-3 : bond 0.00900 ( 8) link_ALPHA1-3 : angle 1.74681 ( 24) hydrogen bonds : bond 0.03259 ( 624) hydrogen bonds : angle 5.78820 ( 1668) link_BETA1-6 : bond 0.00811 ( 2) link_BETA1-6 : angle 1.12393 ( 6) SS BOND : bond 0.00205 ( 44) SS BOND : angle 0.87249 ( 88) covalent geometry : bond 0.00273 (20756) covalent geometry : angle 0.61646 (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 288 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 4.800 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: 0.9052 (mm-30) cc_final: 0.8495 (mp0) REVERT: E 39 GLN cc_start: 0.7652 (tt0) cc_final: 0.7006 (tp40) REVERT: E 46 GLU cc_start: 0.8629 (tt0) cc_final: 0.8098 (tt0) REVERT: E 48 MET cc_start: 0.9259 (mtp) cc_final: 0.9005 (mtm) REVERT: E 65 GLN cc_start: 0.8314 (tt0) cc_final: 0.7781 (mm-40) REVERT: E 73 ASP cc_start: 0.7317 (t0) cc_final: 0.6643 (t0) REVERT: E 107 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8914 (t70) REVERT: F 11 LEU cc_start: 0.8636 (tp) cc_final: 0.8369 (tt) REVERT: F 82 ASP cc_start: 0.8345 (m-30) cc_final: 0.8030 (m-30) REVERT: A 10 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8462 (tp30) REVERT: A 23 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8647 (tttp) REVERT: A 46 GLU cc_start: 0.8631 (tt0) cc_final: 0.8112 (tt0) REVERT: A 65 GLN cc_start: 0.8264 (tt0) cc_final: 0.7678 (mm-40) REVERT: A 73 ASP cc_start: 0.7339 (t0) cc_final: 0.6703 (t0) REVERT: A 77 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 90 ASP cc_start: 0.7716 (m-30) cc_final: 0.7274 (m-30) REVERT: A 107 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8928 (t70) REVERT: D 11 LEU cc_start: 0.8641 (tp) cc_final: 0.8389 (tt) REVERT: D 82 ASP cc_start: 0.8428 (m-30) cc_final: 0.8115 (m-30) REVERT: B 10 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8489 (mp0) REVERT: B 39 GLN cc_start: 0.7669 (tt0) cc_final: 0.7019 (tp40) REVERT: B 46 GLU cc_start: 0.8618 (tt0) cc_final: 0.8097 (tt0) REVERT: B 65 GLN cc_start: 0.8265 (tt0) cc_final: 0.7675 (mm-40) REVERT: B 73 ASP cc_start: 0.7314 (t0) cc_final: 0.6633 (t0) REVERT: B 107 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8930 (t70) REVERT: H 6 GLN cc_start: 0.7822 (tt0) cc_final: 0.7594 (tt0) REVERT: H 11 LEU cc_start: 0.8690 (tp) cc_final: 0.8440 (tt) REVERT: H 39 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8714 (mttm) REVERT: H 82 ASP cc_start: 0.8384 (m-30) cc_final: 0.8133 (m-30) REVERT: H 104 LYS cc_start: 0.8325 (tppt) cc_final: 0.8113 (tppt) REVERT: C 10 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8503 (mp0) REVERT: C 39 GLN cc_start: 0.7662 (tt0) cc_final: 0.7009 (tp40) REVERT: C 46 GLU cc_start: 0.8619 (tt0) cc_final: 0.8092 (tt0) REVERT: C 65 GLN cc_start: 0.8266 (tt0) cc_final: 0.7724 (mm-40) REVERT: C 73 ASP cc_start: 0.7313 (t0) cc_final: 0.6633 (t0) REVERT: C 107 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8906 (t70) REVERT: I 11 LEU cc_start: 0.8640 (tp) cc_final: 0.8370 (tt) REVERT: I 39 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8723 (mttm) REVERT: I 82 ASP cc_start: 0.8408 (m-30) cc_final: 0.8121 (m-30) outliers start: 59 outliers final: 23 residues processed: 259 average time/residue: 2.4694 time to fit residues: 717.7305 Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 23 LYS 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 A residue 107 ASP Chi-restraints excluded: chain D residue 47 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 B residue 107 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 47 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 C residue 107 ASP Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 90 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 192 optimal weight: 0.0970 chunk 229 optimal weight: 0.3980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057714 restraints weight = 40254.210| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.95 r_work: 0.2732 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20876 Z= 0.189 Angle : 0.681 9.459 28498 Z= 0.337 Chirality : 0.046 0.189 3292 Planarity : 0.005 0.046 3534 Dihedral : 7.012 53.602 4264 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 3.27 % Allowed : 11.50 % Favored : 85.23 % 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: -0.38 (0.16), residues: 2488 helix: -0.26 (1.06), residues: 24 sheet: 0.40 (0.16), residues: 1084 loop : -0.78 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 178 HIS 0.004 0.001 HIS G 347 PHE 0.014 0.002 PHE G 410 TYR 0.018 0.001 TYR D 49 ARG 0.011 0.001 ARG D 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 23) link_NAG-ASN : angle 2.32940 ( 69) link_ALPHA1-6 : bond 0.00453 ( 8) link_ALPHA1-6 : angle 1.42553 ( 24) link_BETA1-4 : bond 0.00492 ( 31) link_BETA1-4 : angle 1.67277 ( 93) link_ALPHA1-2 : bond 0.00329 ( 4) link_ALPHA1-2 : angle 2.44663 ( 12) link_ALPHA1-3 : bond 0.00665 ( 8) link_ALPHA1-3 : angle 1.97702 ( 24) hydrogen bonds : bond 0.03574 ( 624) hydrogen bonds : angle 5.81469 ( 1668) link_BETA1-6 : bond 0.00803 ( 2) link_BETA1-6 : angle 1.05603 ( 6) SS BOND : bond 0.00279 ( 44) SS BOND : angle 0.91511 ( 88) covalent geometry : bond 0.00452 (20756) covalent geometry : angle 0.66079 (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 296 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 2.918 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: 0.9075 (mm-30) cc_final: 0.8511 (mp0) REVERT: E 46 GLU cc_start: 0.8551 (tt0) cc_final: 0.8175 (tt0) REVERT: E 65 GLN cc_start: 0.8355 (tt0) cc_final: 0.7779 (mm-40) REVERT: E 73 ASP cc_start: 0.7370 (t0) cc_final: 0.6734 (t0) REVERT: E 77 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7930 (p) REVERT: F 11 LEU cc_start: 0.8666 (tp) cc_final: 0.8409 (tt) REVERT: F 61 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8346 (ptm160) REVERT: F 82 ASP cc_start: 0.8147 (m-30) cc_final: 0.7715 (m-30) REVERT: A 10 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8453 (tp30) REVERT: A 23 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8665 (tttp) REVERT: A 39 GLN cc_start: 0.7695 (tt0) cc_final: 0.7040 (tp40) REVERT: A 46 GLU cc_start: 0.8574 (tt0) cc_final: 0.8152 (tt0) REVERT: A 65 GLN cc_start: 0.8319 (tt0) cc_final: 0.7705 (mm-40) REVERT: A 73 ASP cc_start: 0.7407 (t0) cc_final: 0.6748 (t0) REVERT: D 11 LEU cc_start: 0.8671 (tp) cc_final: 0.8404 (tt) REVERT: B 10 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8502 (mp0) REVERT: B 46 GLU cc_start: 0.8545 (tt0) cc_final: 0.8182 (tt0) REVERT: B 65 GLN cc_start: 0.8318 (tt0) cc_final: 0.7712 (mm-40) REVERT: B 73 ASP cc_start: 0.7371 (t0) cc_final: 0.6734 (t0) REVERT: B 77 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7938 (p) REVERT: H 6 GLN cc_start: 0.7911 (tt0) cc_final: 0.7467 (tt0) REVERT: H 11 LEU cc_start: 0.8693 (tp) cc_final: 0.8434 (tt) REVERT: H 82 ASP cc_start: 0.8425 (m-30) cc_final: 0.8022 (m-30) REVERT: C 10 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8513 (mp0) REVERT: C 46 GLU cc_start: 0.8536 (tt0) cc_final: 0.8165 (tt0) REVERT: C 65 GLN cc_start: 0.8319 (tt0) cc_final: 0.7765 (mm-40) REVERT: C 73 ASP cc_start: 0.7362 (t0) cc_final: 0.6726 (t0) REVERT: C 77 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7930 (p) REVERT: I 6 GLN cc_start: 0.7897 (tt0) cc_final: 0.7453 (tt0) REVERT: I 11 LEU cc_start: 0.8669 (tp) cc_final: 0.8411 (tt) outliers start: 70 outliers final: 22 residues processed: 268 average time/residue: 1.8049 time to fit residues: 541.4264 Evaluate side-chains 234 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 35 SER 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 D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 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 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 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS F 32 ASN F 92 ASN K 347 HIS L 347 HIS I 32 ASN I 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058837 restraints weight = 39842.698| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.93 r_work: 0.2758 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20876 Z= 0.134 Angle : 0.667 10.003 28498 Z= 0.328 Chirality : 0.045 0.186 3292 Planarity : 0.005 0.054 3534 Dihedral : 6.640 49.549 4264 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 2.80 % Allowed : 12.85 % Favored : 84.35 % 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: -0.34 (0.16), residues: 2488 helix: -0.24 (1.05), residues: 24 sheet: 0.45 (0.16), residues: 1060 loop : -0.75 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 178 HIS 0.003 0.001 HIS K 347 PHE 0.013 0.002 PHE J 422 TYR 0.019 0.001 TYR I 49 ARG 0.013 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 23) link_NAG-ASN : angle 2.10482 ( 69) link_ALPHA1-6 : bond 0.00553 ( 8) link_ALPHA1-6 : angle 1.37823 ( 24) link_BETA1-4 : bond 0.00527 ( 31) link_BETA1-4 : angle 1.49693 ( 93) link_ALPHA1-2 : bond 0.00458 ( 4) link_ALPHA1-2 : angle 2.37831 ( 12) link_ALPHA1-3 : bond 0.00887 ( 8) link_ALPHA1-3 : angle 1.77239 ( 24) hydrogen bonds : bond 0.03263 ( 624) hydrogen bonds : angle 5.61894 ( 1668) link_BETA1-6 : bond 0.00746 ( 2) link_BETA1-6 : angle 1.10510 ( 6) SS BOND : bond 0.00251 ( 44) SS BOND : angle 0.98757 ( 88) covalent geometry : bond 0.00314 (20756) covalent geometry : angle 0.64963 (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 285 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 3.245 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: 0.9042 (mm-30) cc_final: 0.8477 (mp0) REVERT: E 23 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8508 (tttp) REVERT: E 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.8100 (tt0) REVERT: E 65 GLN cc_start: 0.8327 (tt0) cc_final: 0.7708 (mm-40) REVERT: E 73 ASP cc_start: 0.7367 (t0) cc_final: 0.6735 (t0) REVERT: E 77 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7919 (p) REVERT: E 87 ARG cc_start: 0.7403 (mtm110) cc_final: 0.6802 (ptp-110) REVERT: E 90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7684 (m-30) REVERT: F 11 LEU cc_start: 0.8655 (tp) cc_final: 0.8384 (tt) REVERT: F 61 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8186 (ptm160) REVERT: A 10 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8404 (tp30) REVERT: A 46 GLU cc_start: 0.8587 (tt0) cc_final: 0.8016 (tt0) REVERT: A 48 MET cc_start: 0.9171 (mtp) cc_final: 0.8950 (mtm) REVERT: A 65 GLN cc_start: 0.8309 (tt0) cc_final: 0.7701 (mm-40) REVERT: A 73 ASP cc_start: 0.7452 (t0) cc_final: 0.6867 (t0) REVERT: D 11 LEU cc_start: 0.8619 (tp) cc_final: 0.8356 (tt) REVERT: D 82 ASP cc_start: 0.8155 (m-30) cc_final: 0.7780 (m-30) REVERT: B 10 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8468 (mp0) REVERT: B 23 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8512 (tttp) REVERT: B 46 GLU cc_start: 0.8615 (tt0) cc_final: 0.8102 (tt0) REVERT: B 65 GLN cc_start: 0.8323 (tt0) cc_final: 0.7762 (mm-40) REVERT: B 73 ASP cc_start: 0.7366 (t0) cc_final: 0.6734 (t0) REVERT: B 77 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 87 ARG cc_start: 0.7401 (mtm110) cc_final: 0.6792 (ptp-110) REVERT: B 90 ASP cc_start: 0.7983 (m-30) cc_final: 0.7674 (m-30) REVERT: H 11 LEU cc_start: 0.8670 (tp) cc_final: 0.8408 (tt) REVERT: H 82 ASP cc_start: 0.8438 (m-30) cc_final: 0.8084 (m-30) REVERT: C 10 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8481 (mp0) REVERT: C 23 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8507 (tttp) REVERT: C 46 GLU cc_start: 0.8608 (tt0) cc_final: 0.8087 (tt0) REVERT: C 65 GLN cc_start: 0.8336 (tt0) cc_final: 0.7774 (mm-40) REVERT: C 73 ASP cc_start: 0.7350 (t0) cc_final: 0.6718 (t0) REVERT: C 77 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7917 (p) REVERT: C 87 ARG cc_start: 0.7402 (mtm110) cc_final: 0.6791 (ptp-110) REVERT: C 90 ASP cc_start: 0.7950 (m-30) cc_final: 0.7638 (m-30) REVERT: I 11 LEU cc_start: 0.8665 (tp) cc_final: 0.8401 (tt) REVERT: I 39 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8722 (mttm) outliers start: 60 outliers final: 30 residues processed: 264 average time/residue: 2.3385 time to fit residues: 685.8079 Evaluate side-chains 246 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 23 LYS 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 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain 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 390 LEU 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 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 390 LEU 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 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058035 restraints weight = 40392.663| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.95 r_work: 0.2737 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20876 Z= 0.175 Angle : 0.685 10.121 28498 Z= 0.336 Chirality : 0.046 0.188 3292 Planarity : 0.005 0.055 3534 Dihedral : 6.739 50.551 4264 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 2.71 % Allowed : 13.74 % Favored : 83.55 % 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: -0.40 (0.16), residues: 2488 helix: -0.28 (1.06), residues: 24 sheet: 0.44 (0.16), residues: 1060 loop : -0.82 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 178 HIS 0.004 0.001 HIS J 184 PHE 0.013 0.002 PHE L 410 TYR 0.019 0.001 TYR D 49 ARG 0.013 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 23) link_NAG-ASN : angle 2.23327 ( 69) link_ALPHA1-6 : bond 0.00469 ( 8) link_ALPHA1-6 : angle 1.42511 ( 24) link_BETA1-4 : bond 0.00491 ( 31) link_BETA1-4 : angle 1.58816 ( 93) link_ALPHA1-2 : bond 0.00336 ( 4) link_ALPHA1-2 : angle 2.42483 ( 12) link_ALPHA1-3 : bond 0.00693 ( 8) link_ALPHA1-3 : angle 1.94534 ( 24) hydrogen bonds : bond 0.03483 ( 624) hydrogen bonds : angle 5.63661 ( 1668) link_BETA1-6 : bond 0.00726 ( 2) link_BETA1-6 : angle 1.06640 ( 6) SS BOND : bond 0.00276 ( 44) SS BOND : angle 1.01252 ( 88) covalent geometry : bond 0.00418 (20756) covalent geometry : angle 0.66521 (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 268 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 2.426 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: 0.9080 (mm-30) cc_final: 0.8548 (mp0) REVERT: E 23 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: E 46 GLU cc_start: 0.8619 (tt0) cc_final: 0.8204 (tt0) REVERT: E 65 GLN cc_start: 0.8359 (tt0) cc_final: 0.7774 (mm-40) REVERT: E 73 ASP cc_start: 0.7440 (t0) cc_final: 0.6853 (t0) REVERT: E 98 ARG cc_start: 0.8856 (ptp-110) cc_final: 0.8575 (ptm160) REVERT: F 11 LEU cc_start: 0.8680 (tp) cc_final: 0.8413 (tt) REVERT: F 82 ASP cc_start: 0.8621 (m-30) cc_final: 0.7910 (m-30) REVERT: A 10 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8445 (mp0) REVERT: A 12 LYS cc_start: 0.9230 (mmtp) cc_final: 0.8819 (mmmm) REVERT: A 46 GLU cc_start: 0.8617 (tt0) cc_final: 0.8135 (tt0) REVERT: A 65 GLN cc_start: 0.8355 (tt0) cc_final: 0.7754 (mm-40) REVERT: A 73 ASP cc_start: 0.7460 (t0) cc_final: 0.6884 (t0) REVERT: D 11 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8408 (tt) REVERT: D 18 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8713 (tpp80) REVERT: D 78 LEU cc_start: 0.8475 (mm) cc_final: 0.8272 (mm) REVERT: B 10 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8535 (mp0) REVERT: B 23 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: B 46 GLU cc_start: 0.8623 (tt0) cc_final: 0.8208 (tt0) REVERT: B 65 GLN cc_start: 0.8391 (tt0) cc_final: 0.7806 (mm-40) REVERT: B 73 ASP cc_start: 0.7438 (t0) cc_final: 0.6852 (t0) REVERT: B 98 ARG cc_start: 0.8857 (ptp-110) cc_final: 0.8576 (ptm160) REVERT: H 11 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8428 (tt) REVERT: H 82 ASP cc_start: 0.8409 (m-30) cc_final: 0.8034 (m-30) REVERT: C 10 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8552 (mp0) REVERT: C 23 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: C 46 GLU cc_start: 0.8609 (tt0) cc_final: 0.8192 (tt0) REVERT: C 65 GLN cc_start: 0.8395 (tt0) cc_final: 0.7819 (mm-40) REVERT: C 73 ASP cc_start: 0.7428 (t0) cc_final: 0.6844 (t0) REVERT: C 98 ARG cc_start: 0.8859 (ptp-110) cc_final: 0.8574 (ptm160) REVERT: I 11 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8423 (tt) REVERT: I 18 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8713 (tpp80) outliers start: 58 outliers final: 26 residues processed: 245 average time/residue: 1.5913 time to fit residues: 436.2827 Evaluate side-chains 235 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 23 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 11 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 23 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 51 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058068 restraints weight = 40302.051| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.95 r_work: 0.2737 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20876 Z= 0.175 Angle : 0.695 10.632 28498 Z= 0.339 Chirality : 0.046 0.190 3292 Planarity : 0.005 0.065 3534 Dihedral : 6.727 50.581 4264 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 1.96 % Allowed : 14.95 % Favored : 83.08 % 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: -0.44 (0.16), residues: 2488 helix: -0.31 (1.05), residues: 24 sheet: 0.40 (0.16), residues: 1068 loop : -0.84 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 178 HIS 0.004 0.001 HIS L 184 PHE 0.013 0.002 PHE L 410 TYR 0.021 0.001 TYR H 49 ARG 0.015 0.001 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 23) link_NAG-ASN : angle 2.21328 ( 69) link_ALPHA1-6 : bond 0.00461 ( 8) link_ALPHA1-6 : angle 1.42599 ( 24) link_BETA1-4 : bond 0.00498 ( 31) link_BETA1-4 : angle 1.56740 ( 93) link_ALPHA1-2 : bond 0.00336 ( 4) link_ALPHA1-2 : angle 2.51486 ( 12) link_ALPHA1-3 : bond 0.00695 ( 8) link_ALPHA1-3 : angle 1.93574 ( 24) hydrogen bonds : bond 0.03489 ( 624) hydrogen bonds : angle 5.62084 ( 1668) link_BETA1-6 : bond 0.00685 ( 2) link_BETA1-6 : angle 1.06167 ( 6) SS BOND : bond 0.00293 ( 44) SS BOND : angle 0.96060 ( 88) covalent geometry : bond 0.00418 (20756) covalent geometry : angle 0.67669 (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 256 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 2.462 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: E 10 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8547 (mp0) REVERT: E 23 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8486 (tttp) REVERT: E 46 GLU cc_start: 0.8676 (tt0) cc_final: 0.8130 (tt0) REVERT: E 65 GLN cc_start: 0.8433 (tt0) cc_final: 0.7838 (mm-40) REVERT: E 73 ASP cc_start: 0.7514 (t0) cc_final: 0.6929 (t0) REVERT: F 4 MET cc_start: 0.7692 (tpp) cc_final: 0.7399 (mmm) REVERT: F 18 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8758 (tpp80) REVERT: A 10 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8468 (tp30) REVERT: A 23 LYS cc_start: 0.8762 (tptt) cc_final: 0.8554 (tttp) REVERT: A 46 GLU cc_start: 0.8718 (tt0) cc_final: 0.8152 (tt0) REVERT: A 65 GLN cc_start: 0.8441 (tt0) cc_final: 0.7921 (mm-40) REVERT: A 73 ASP cc_start: 0.7503 (t0) cc_final: 0.6905 (t0) REVERT: D 4 MET cc_start: 0.7672 (tpp) cc_final: 0.7406 (mmm) REVERT: D 11 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8404 (tt) REVERT: D 18 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8778 (tpp80) REVERT: B 10 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8552 (mp0) REVERT: B 23 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8481 (tttp) REVERT: B 46 GLU cc_start: 0.8751 (tt0) cc_final: 0.8218 (tt0) REVERT: B 65 GLN cc_start: 0.8439 (tt0) cc_final: 0.7830 (mm-40) REVERT: B 73 ASP cc_start: 0.7507 (t0) cc_final: 0.6923 (t0) REVERT: H 4 MET cc_start: 0.7667 (tpp) cc_final: 0.7388 (mmm) REVERT: H 11 LEU cc_start: 0.8683 (tp) cc_final: 0.8415 (tt) REVERT: H 18 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8690 (tpp80) REVERT: H 82 ASP cc_start: 0.8454 (m-30) cc_final: 0.8094 (m-30) REVERT: C 10 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8551 (mp0) REVERT: C 23 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8487 (tttp) REVERT: C 46 GLU cc_start: 0.8662 (tt0) cc_final: 0.8103 (tt0) REVERT: C 65 GLN cc_start: 0.8442 (tt0) cc_final: 0.7846 (mm-40) REVERT: C 73 ASP cc_start: 0.7503 (t0) cc_final: 0.6921 (t0) REVERT: C 98 ARG cc_start: 0.8856 (ptp-110) cc_final: 0.8656 (ptm160) REVERT: I 4 MET cc_start: 0.7675 (tpp) cc_final: 0.7412 (mmm) REVERT: I 11 LEU cc_start: 0.8649 (tp) cc_final: 0.8395 (tt) REVERT: I 18 ARG cc_start: 0.9159 (tpp80) cc_final: 0.8862 (tpp80) outliers start: 42 outliers final: 23 residues processed: 234 average time/residue: 1.7174 time to fit residues: 444.9525 Evaluate side-chains 237 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 2.950 ------------------------------------------------------------------------------- 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 23 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 11 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 23 LYS 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 23 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG 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: 8.9990 chunk 246 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056870 restraints weight = 40273.012| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.91 r_work: 0.2714 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20876 Z= 0.253 Angle : 0.751 11.248 28498 Z= 0.367 Chirality : 0.048 0.187 3292 Planarity : 0.005 0.055 3534 Dihedral : 7.224 55.848 4264 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 1.50 % Allowed : 15.47 % Favored : 83.04 % 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: -0.59 (0.16), residues: 2488 helix: -0.32 (1.08), residues: 24 sheet: 0.36 (0.16), residues: 1060 loop : -1.00 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 178 HIS 0.005 0.001 HIS G 184 PHE 0.017 0.002 PHE L 410 TYR 0.023 0.002 TYR D 49 ARG 0.014 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 23) link_NAG-ASN : angle 2.47297 ( 69) link_ALPHA1-6 : bond 0.00315 ( 8) link_ALPHA1-6 : angle 1.48261 ( 24) link_BETA1-4 : bond 0.00474 ( 31) link_BETA1-4 : angle 1.77698 ( 93) link_ALPHA1-2 : bond 0.00166 ( 4) link_ALPHA1-2 : angle 2.63336 ( 12) link_ALPHA1-3 : bond 0.00471 ( 8) link_ALPHA1-3 : angle 2.23712 ( 24) hydrogen bonds : bond 0.03913 ( 624) hydrogen bonds : angle 5.73438 ( 1668) link_BETA1-6 : bond 0.00800 ( 2) link_BETA1-6 : angle 1.06738 ( 6) SS BOND : bond 0.00357 ( 44) SS BOND : angle 1.13335 ( 88) covalent geometry : bond 0.00607 (20756) covalent geometry : angle 0.72878 (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 241 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8565 (mp0) REVERT: E 23 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (tttp) REVERT: E 46 GLU cc_start: 0.8769 (tt0) cc_final: 0.8262 (tt0) REVERT: E 65 GLN cc_start: 0.8531 (tt0) cc_final: 0.7962 (mm-40) REVERT: E 73 ASP cc_start: 0.7600 (t0) cc_final: 0.7020 (t0) REVERT: F 18 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8812 (tpp80) REVERT: A 10 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8503 (tp30) REVERT: A 23 LYS cc_start: 0.8796 (tptt) cc_final: 0.8593 (tttp) REVERT: A 46 GLU cc_start: 0.8780 (tt0) cc_final: 0.8245 (tt0) REVERT: A 65 GLN cc_start: 0.8501 (tt0) cc_final: 0.7985 (mm-40) REVERT: A 73 ASP cc_start: 0.7601 (t0) cc_final: 0.7030 (t0) REVERT: D 18 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8872 (tpp80) REVERT: B 10 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 23 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8550 (tttp) REVERT: B 46 GLU cc_start: 0.8772 (tt0) cc_final: 0.8264 (tt0) REVERT: B 65 GLN cc_start: 0.8541 (tt0) cc_final: 0.7966 (mm-40) REVERT: B 73 ASP cc_start: 0.7582 (t0) cc_final: 0.7004 (t0) REVERT: H 82 ASP cc_start: 0.8573 (m-30) cc_final: 0.8164 (m-30) REVERT: C 10 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8563 (mp0) REVERT: C 23 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8570 (tptp) REVERT: C 46 GLU cc_start: 0.8779 (tt0) cc_final: 0.8252 (tt0) REVERT: C 65 GLN cc_start: 0.8542 (tt0) cc_final: 0.7979 (mm-40) REVERT: C 73 ASP cc_start: 0.7581 (t0) cc_final: 0.7001 (t0) REVERT: I 18 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8910 (tpp80) outliers start: 32 outliers final: 21 residues processed: 229 average time/residue: 1.6420 time to fit residues: 417.0604 Evaluate side-chains 230 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 23 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 51 ILE 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 23 LYS 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 23 LYS 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: 0.9980 chunk 19 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058599 restraints weight = 40105.713| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.93 r_work: 0.2754 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3293 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= 0.132 Angle : 0.684 11.428 28498 Z= 0.331 Chirality : 0.045 0.187 3292 Planarity : 0.005 0.067 3534 Dihedral : 6.597 49.182 4264 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.59 % Allowed : 15.51 % Favored : 82.90 % 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: -0.44 (0.16), residues: 2488 helix: -0.33 (1.01), residues: 24 sheet: 0.42 (0.16), residues: 1068 loop : -0.86 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 178 HIS 0.003 0.001 HIS K 184 PHE 0.013 0.002 PHE G 422 TYR 0.021 0.001 TYR H 49 ARG 0.015 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 23) link_NAG-ASN : angle 2.02725 ( 69) link_ALPHA1-6 : bond 0.00574 ( 8) link_ALPHA1-6 : angle 1.37996 ( 24) link_BETA1-4 : bond 0.00557 ( 31) link_BETA1-4 : angle 1.44368 ( 93) link_ALPHA1-2 : bond 0.00460 ( 4) link_ALPHA1-2 : angle 2.48428 ( 12) link_ALPHA1-3 : bond 0.00926 ( 8) link_ALPHA1-3 : angle 1.76878 ( 24) hydrogen bonds : bond 0.03253 ( 624) hydrogen bonds : angle 5.55353 ( 1668) link_BETA1-6 : bond 0.00654 ( 2) link_BETA1-6 : angle 1.09283 ( 6) SS BOND : bond 0.00271 ( 44) SS BOND : angle 0.84110 ( 88) covalent geometry : bond 0.00309 (20756) covalent geometry : angle 0.66848 (28182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19703.14 seconds wall clock time: 348 minutes 22.59 seconds (20902.59 seconds total)