Starting phenix.real_space_refine on Sat Jul 4 11:44:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_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_29705/07_2026/8g3n_29705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3n_29705/07_2026/8g3n_29705.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12564 2.51 5 N 3434 2.21 5 O 4202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 39 Chain: "G" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 4.58, per 1000 atoms: 0.23 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: 1.73 Conformation dependent library (CDL) restraints added in 774.1 milliseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4552 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 44 sheets defined 4.1% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 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: 4.03 Time building geometry restraints manager: 2.19 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 - 17.49: 10884 17.49 - 34.98: 673 34.98 - 52.46: 115 52.46 - 69.95: 36 69.95 - 87.44: 20 Dihedral angle restraints: 11728 sinusoidal: 4584 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 11725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1382 0.055 - 0.110: 1063 0.110 - 0.164: 602 0.164 - 0.219: 179 0.219 - 0.274: 66 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.28e+01 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.97e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.95e+01 ... (remaining 3289 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP J 115 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP J 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP J 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP J 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP K 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP K 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP K 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP K 115 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP K 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP K 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 115 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP K 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.12e+01 pdb=" CG TRP G 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP G 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP G 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP G 115 " 0.051 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3843 2.82 - 3.34: 18780 3.34 - 3.86: 32203 3.86 - 4.38: 41311 4.38 - 4.90: 68081 Nonbonded interactions: 164218 Sorted by model distance: nonbonded pdb=" O HIS L 347 " pdb="CA CA L2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS K 347 " pdb="CA CA K2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.303 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.303 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J2000 " model vdw 2.342 2.510 ... (remaining 164213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'G' and resid 82 through 501) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.310 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 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 : 12.889 87.439 7044 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 2488 helix: -1.68 (0.62), residues: 24 sheet: 0.32 (0.16), residues: 980 loop : -0.92 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG L 156 TYR 0.058 0.012 TYR J 121 PHE 0.062 0.012 PHE L 205 TRP 0.113 0.014 TRP J 115 HIS 0.032 0.005 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01636 / 1.15 (20756) covalent geometry : angle 1.75532 / 1.15 (28182) SS BOND : bond 0.08872 / 6.16 ( 44) SS BOND : angle 2.97254 / 2.12 ( 88) hydrogen bonds : bond 0.14918 / 9.77 ( 624) hydrogen bonds : angle 8.16693 / 5.76 ( 1668) link_ALPHA1-2 : bond 0.00279 / 0.13 ( 4) link_ALPHA1-2 : angle 5.04486 / 3.00 ( 12) link_ALPHA1-3 : bond 0.01567 / 0.96 ( 8) link_ALPHA1-3 : angle 3.88316 / 2.38 ( 24) link_ALPHA1-6 : bond 0.02024 / 1.25 ( 8) link_ALPHA1-6 : angle 3.12059 / 1.89 ( 24) link_BETA1-4 : bond 0.02144 / 1.32 ( 31) link_BETA1-4 : angle 4.18769 / 3.07 ( 93) link_BETA1-6 : bond 0.01864 / 0.94 ( 2) link_BETA1-6 : angle 4.41534 / 2.75 ( 6) link_NAG-ASN : bond 0.00626 / 0.39 ( 23) link_NAG-ASN : angle 5.33814 / 3.66 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ASP cc_start: 0.7076 (t0) cc_final: 0.6734 (t0) REVERT: F 85 ILE cc_start: 0.8678 (tt) cc_final: 0.8459 (tp) REVERT: A 10 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8290 (tp30) REVERT: A 73 ASP cc_start: 0.7079 (t0) cc_final: 0.6737 (t0) REVERT: D 85 ILE cc_start: 0.8673 (tt) cc_final: 0.8453 (tp) REVERT: B 73 ASP cc_start: 0.7074 (t0) cc_final: 0.6732 (t0) REVERT: H 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8458 (tp) REVERT: C 73 ASP cc_start: 0.7071 (t0) cc_final: 0.6728 (t0) REVERT: I 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8458 (tp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.7476 time to fit residues: 226.9781 Evaluate side-chains 204 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3562 r_free = 0.3562 target = 0.092700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060881 restraints weight = 39347.453| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.90 r_work: 0.2796 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20876 Z= 0.141 Angle : 0.697 7.982 28498 Z= 0.360 Chirality : 0.046 0.161 3292 Planarity : 0.004 0.067 3534 Dihedral : 5.876 24.475 2732 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.20 % Allowed : 9.49 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2488 helix: -0.30 (0.96), residues: 24 sheet: 0.22 (0.15), residues: 1100 loop : -0.66 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.012 0.001 TYR F 49 PHE 0.012 0.002 PHE G 410 TRP 0.022 0.002 TRP J 178 HIS 0.004 0.001 HIS L 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (20756) covalent geometry : angle 0.67362 / 0.36 (28182) SS BOND : bond 0.00392 / 0.20 ( 44) SS BOND : angle 1.08970 / 0.78 ( 88) hydrogen bonds : bond 0.04022 / 2.65 ( 624) hydrogen bonds : angle 6.58517 / 4.63 ( 1668) link_ALPHA1-2 : bond 0.00560 / 0.25 ( 4) link_ALPHA1-2 : angle 1.87221 / 1.01 ( 12) link_ALPHA1-3 : bond 0.00886 / 0.57 ( 8) link_ALPHA1-3 : angle 1.66876 / 1.03 ( 24) link_ALPHA1-6 : bond 0.00523 / 0.32 ( 8) link_ALPHA1-6 : angle 1.21609 / 0.74 ( 24) link_BETA1-4 : bond 0.00586 / 0.36 ( 31) link_BETA1-4 : angle 1.89889 / 1.30 ( 93) link_BETA1-6 : bond 0.01100 / 0.57 ( 2) link_BETA1-6 : angle 1.06390 / 0.62 ( 6) link_NAG-ASN : bond 0.00543 / 0.31 ( 23) link_NAG-ASN : angle 2.63486 / 1.73 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8772 (ttt) cc_final: 0.8507 (ttp) REVERT: E 10 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8323 (mp0) REVERT: E 23 LYS cc_start: 0.8642 (tttp) cc_final: 0.8423 (tttp) REVERT: E 73 ASP cc_start: 0.7188 (t0) cc_final: 0.6615 (t0) REVERT: F 61 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7381 (ptm160) REVERT: F 70 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7414 (mm-30) REVERT: F 79 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7702 (mp-120) REVERT: F 81 GLU cc_start: 0.8470 (pm20) cc_final: 0.8269 (pm20) REVERT: F 82 ASP cc_start: 0.8431 (m-30) cc_final: 0.7191 (m-30) REVERT: F 106 GLU cc_start: 0.6234 (tm-30) cc_final: 0.6015 (tm-30) REVERT: J 160 MET cc_start: 0.8774 (ttt) cc_final: 0.8511 (ttp) REVERT: A 10 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8268 (tp30) REVERT: A 23 LYS cc_start: 0.8666 (tttp) cc_final: 0.8320 (tttp) REVERT: A 65 GLN cc_start: 0.8262 (tt0) cc_final: 0.7709 (mt0) REVERT: A 73 ASP cc_start: 0.7203 (t0) cc_final: 0.6633 (t0) REVERT: D 61 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7474 (ptm160) REVERT: D 70 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 79 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7699 (mp-120) REVERT: D 82 ASP cc_start: 0.8442 (m-30) cc_final: 0.7159 (m-30) REVERT: D 106 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5999 (tm-30) REVERT: K 160 MET cc_start: 0.8769 (ttt) cc_final: 0.8498 (ttp) REVERT: B 10 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8296 (mp0) REVERT: B 23 LYS cc_start: 0.8650 (tttp) cc_final: 0.8434 (tttp) REVERT: B 73 ASP cc_start: 0.7149 (t0) cc_final: 0.6578 (t0) REVERT: H 61 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: H 70 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7407 (mm-30) REVERT: H 79 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7705 (mp-120) REVERT: H 82 ASP cc_start: 0.8425 (m-30) cc_final: 0.7194 (m-30) REVERT: L 160 MET cc_start: 0.8774 (ttt) cc_final: 0.8509 (ttp) REVERT: C 10 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8314 (mp0) REVERT: C 23 LYS cc_start: 0.8642 (tttp) cc_final: 0.8423 (tttp) REVERT: C 73 ASP cc_start: 0.7180 (t0) cc_final: 0.6609 (t0) REVERT: I 61 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: I 70 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7403 (mm-30) REVERT: I 79 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7698 (mp-120) REVERT: I 81 GLU cc_start: 0.8462 (pm20) cc_final: 0.8261 (pm20) REVERT: I 82 ASP cc_start: 0.8415 (m-30) cc_final: 0.7174 (m-30) REVERT: I 106 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6026 (tm-30) outliers start: 47 outliers final: 4 residues processed: 256 average time/residue: 0.7130 time to fit residues: 201.4529 Evaluate side-chains 204 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 GLN F 93 ASN A 39 GLN D 93 ASN B 39 GLN H 93 ASN C 39 GLN I 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059018 restraints weight = 39914.967| |-----------------------------------------------------------------------------| r_work (start): 0.2890 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: 0.8820 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20876 Z= 0.161 Angle : 0.656 7.778 28498 Z= 0.334 Chirality : 0.046 0.150 3292 Planarity : 0.004 0.039 3534 Dihedral : 5.401 24.464 2732 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.94 % Allowed : 9.67 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2488 helix: -0.10 (1.07), residues: 24 sheet: 0.37 (0.15), residues: 1072 loop : -0.72 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 45 TYR 0.018 0.002 TYR J 121 PHE 0.013 0.002 PHE K 410 TRP 0.021 0.001 TRP L 178 HIS 0.005 0.001 HIS L 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (20756) covalent geometry : angle 0.63222 / 0.33 (28182) SS BOND : bond 0.00323 / 0.15 ( 44) SS BOND : angle 1.14361 / 0.82 ( 88) hydrogen bonds : bond 0.03861 / 2.55 ( 624) hydrogen bonds : angle 6.20129 / 4.35 ( 1668) link_ALPHA1-2 : bond 0.00465 / 0.21 ( 4) link_ALPHA1-2 : angle 2.05169 / 1.08 ( 12) link_ALPHA1-3 : bond 0.00520 / 0.32 ( 8) link_ALPHA1-3 : angle 1.50043 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00364 / 0.22 ( 8) link_ALPHA1-6 : angle 1.45268 / 0.86 ( 24) link_BETA1-4 : bond 0.00538 / 0.33 ( 31) link_BETA1-4 : angle 1.74328 / 1.20 ( 93) link_BETA1-6 : bond 0.01090 / 0.55 ( 2) link_BETA1-6 : angle 1.12328 / 0.67 ( 6) link_NAG-ASN : bond 0.00334 / 0.18 ( 23) link_NAG-ASN : angle 2.48548 / 1.62 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 0.716 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: 0.8939 (mm-30) cc_final: 0.8373 (mp0) REVERT: E 23 LYS cc_start: 0.8622 (tttp) cc_final: 0.8137 (tttp) REVERT: E 65 GLN cc_start: 0.8243 (tt0) cc_final: 0.7589 (mt0) REVERT: E 73 ASP cc_start: 0.7186 (t0) cc_final: 0.6580 (t0) REVERT: E 77 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7857 (p) REVERT: F 6 GLN cc_start: 0.7801 (tt0) cc_final: 0.7595 (tt0) REVERT: F 11 LEU cc_start: 0.8644 (tp) cc_final: 0.8384 (tt) REVERT: F 70 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7409 (mm-30) REVERT: F 82 ASP cc_start: 0.8522 (m-30) cc_final: 0.7699 (m-30) REVERT: F 104 LYS cc_start: 0.8082 (tptt) cc_final: 0.7621 (tppt) REVERT: A 10 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8390 (tp30) REVERT: A 23 LYS cc_start: 0.8637 (tttp) cc_final: 0.8166 (tttp) REVERT: A 65 GLN cc_start: 0.8226 (tt0) cc_final: 0.7613 (mt0) REVERT: A 73 ASP cc_start: 0.7191 (t0) cc_final: 0.6594 (t0) REVERT: D 11 LEU cc_start: 0.8624 (tp) cc_final: 0.8349 (tt) REVERT: D 70 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 82 ASP cc_start: 0.8544 (m-30) cc_final: 0.8271 (m-30) REVERT: B 10 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8424 (mp0) REVERT: B 12 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8915 (mmmm) REVERT: B 23 LYS cc_start: 0.8630 (tttp) cc_final: 0.8017 (tttp) REVERT: B 65 GLN cc_start: 0.8229 (tt0) cc_final: 0.7570 (mt0) REVERT: B 73 ASP cc_start: 0.7167 (t0) cc_final: 0.6566 (t0) REVERT: B 77 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (p) REVERT: H 6 GLN cc_start: 0.7783 (tt0) cc_final: 0.7549 (tt0) REVERT: H 11 LEU cc_start: 0.8656 (tp) cc_final: 0.8379 (tt) REVERT: H 70 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7436 (mm-30) REVERT: H 82 ASP cc_start: 0.8505 (m-30) cc_final: 0.8233 (m-30) REVERT: C 10 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8438 (mp0) REVERT: C 12 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8917 (mmmm) REVERT: C 23 LYS cc_start: 0.8602 (tttp) cc_final: 0.7992 (tttp) REVERT: C 65 GLN cc_start: 0.8229 (tt0) cc_final: 0.7667 (mt0) REVERT: C 73 ASP cc_start: 0.7185 (t0) cc_final: 0.6577 (t0) REVERT: C 77 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (p) REVERT: I 6 GLN cc_start: 0.7776 (tt0) cc_final: 0.7536 (tt0) REVERT: I 11 LEU cc_start: 0.8639 (tp) cc_final: 0.8356 (tt) REVERT: I 70 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7434 (mm-30) REVERT: I 82 ASP cc_start: 0.8509 (m-30) cc_final: 0.7688 (m-30) outliers start: 63 outliers final: 18 residues processed: 249 average time/residue: 0.6960 time to fit residues: 192.0784 Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 173 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058266 restraints weight = 40106.355| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.93 r_work: 0.2742 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20876 Z= 0.178 Angle : 0.652 7.394 28498 Z= 0.329 Chirality : 0.046 0.145 3292 Planarity : 0.004 0.038 3534 Dihedral : 5.183 23.988 2732 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 4.02 % Allowed : 9.86 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2488 helix: -0.14 (1.06), residues: 24 sheet: 0.44 (0.16), residues: 1064 loop : -0.75 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.016 0.001 TYR K 121 PHE 0.014 0.002 PHE L 410 TRP 0.021 0.001 TRP L 178 HIS 0.005 0.001 HIS J 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (20756) covalent geometry : angle 0.63098 / 0.33 (28182) SS BOND : bond 0.00283 / 0.14 ( 44) SS BOND : angle 1.05068 / 0.74 ( 88) hydrogen bonds : bond 0.03716 / 2.45 ( 624) hydrogen bonds : angle 5.99339 / 4.21 ( 1668) link_ALPHA1-2 : bond 0.00431 / 0.20 ( 4) link_ALPHA1-2 : angle 2.15129 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00385 / 0.24 ( 8) link_ALPHA1-3 : angle 1.55481 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00311 / 0.19 ( 8) link_ALPHA1-6 : angle 1.50820 / 0.90 ( 24) link_BETA1-4 : bond 0.00424 / 0.26 ( 31) link_BETA1-4 : angle 1.64506 / 1.12 ( 93) link_BETA1-6 : bond 0.00799 / 0.40 ( 2) link_BETA1-6 : angle 1.08643 / 0.65 ( 6) link_NAG-ASN : bond 0.00319 / 0.18 ( 23) link_NAG-ASN : angle 2.31728 / 1.49 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 227 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8554 (ttt) REVERT: E 10 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8460 (mp0) REVERT: E 23 LYS cc_start: 0.8670 (tttp) cc_final: 0.8171 (tttp) REVERT: E 39 GLN cc_start: 0.7598 (tt0) cc_final: 0.6964 (tp40) REVERT: E 65 GLN cc_start: 0.8246 (tt0) cc_final: 0.7655 (mm-40) REVERT: E 73 ASP cc_start: 0.7287 (t0) cc_final: 0.6657 (t0) REVERT: E 77 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7849 (p) REVERT: F 6 GLN cc_start: 0.7613 (tt0) cc_final: 0.7385 (tt0) REVERT: F 11 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8372 (tt) REVERT: F 82 ASP cc_start: 0.8560 (m-30) cc_final: 0.8254 (m-30) REVERT: J 160 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (ttt) REVERT: A 10 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8414 (tp30) REVERT: A 65 GLN cc_start: 0.8221 (tt0) cc_final: 0.7684 (mm-40) REVERT: A 73 ASP cc_start: 0.7330 (t0) cc_final: 0.6701 (t0) REVERT: A 87 ARG cc_start: 0.7501 (mtm110) cc_final: 0.6871 (ptp-110) REVERT: A 90 ASP cc_start: 0.7933 (m-30) cc_final: 0.7614 (m-30) REVERT: D 11 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 70 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7578 (mm-30) REVERT: D 81 GLU cc_start: 0.8632 (pm20) cc_final: 0.8412 (pm20) REVERT: D 82 ASP cc_start: 0.8607 (m-30) cc_final: 0.8167 (m-30) REVERT: D 104 LYS cc_start: 0.8474 (tppt) cc_final: 0.8256 (tppt) REVERT: K 160 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8559 (ttt) REVERT: B 10 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8462 (mp0) REVERT: B 23 LYS cc_start: 0.8691 (tttp) cc_final: 0.8201 (tttp) REVERT: B 39 GLN cc_start: 0.7613 (tt0) cc_final: 0.6976 (tp40) REVERT: B 65 GLN cc_start: 0.8245 (tt0) cc_final: 0.7647 (mm-40) REVERT: B 73 ASP cc_start: 0.7280 (t0) cc_final: 0.6651 (t0) REVERT: B 77 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (p) REVERT: H 6 GLN cc_start: 0.7644 (tt0) cc_final: 0.7412 (tt0) REVERT: H 11 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8362 (tt) REVERT: H 82 ASP cc_start: 0.8589 (m-30) cc_final: 0.8224 (m-30) REVERT: H 104 LYS cc_start: 0.8489 (tppt) cc_final: 0.8287 (tppt) REVERT: L 160 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (ttt) REVERT: C 10 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8480 (mp0) REVERT: C 23 LYS cc_start: 0.8686 (tttp) cc_final: 0.8170 (tttp) REVERT: C 39 GLN cc_start: 0.7610 (tt0) cc_final: 0.6973 (tp40) REVERT: C 65 GLN cc_start: 0.8253 (tt0) cc_final: 0.7676 (mm-40) REVERT: C 73 ASP cc_start: 0.7290 (t0) cc_final: 0.6657 (t0) REVERT: C 77 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7851 (p) REVERT: I 11 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8351 (tt) REVERT: I 70 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7559 (mm-30) REVERT: I 82 ASP cc_start: 0.8540 (m-30) cc_final: 0.8231 (m-30) REVERT: I 104 LYS cc_start: 0.8463 (tppt) cc_final: 0.8249 (tppt) outliers start: 86 outliers final: 17 residues processed: 276 average time/residue: 0.6991 time to fit residues: 214.0133 Evaluate side-chains 243 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 347 HIS J 347 HIS A 39 GLN D 6 GLN K 347 HIS L 347 HIS I 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.057073 restraints weight = 40150.457| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.90 r_work: 0.2714 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 20876 Z= 0.238 Angle : 0.693 8.239 28498 Z= 0.349 Chirality : 0.047 0.143 3292 Planarity : 0.005 0.046 3534 Dihedral : 5.287 24.223 2732 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 2.57 % Allowed : 11.12 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2488 helix: -0.16 (1.10), residues: 24 sheet: 0.43 (0.16), residues: 1064 loop : -0.84 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 63 TYR 0.019 0.002 TYR J 121 PHE 0.016 0.002 PHE L 410 TRP 0.021 0.002 TRP K 178 HIS 0.006 0.002 HIS L 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (20756) covalent geometry : angle 0.67041 / 0.34 (28182) SS BOND : bond 0.00325 / 0.17 ( 44) SS BOND : angle 1.18507 / 0.80 ( 88) hydrogen bonds : bond 0.03936 / 2.60 ( 624) hydrogen bonds : angle 5.99167 / 4.21 ( 1668) link_ALPHA1-2 : bond 0.00292 / 0.13 ( 4) link_ALPHA1-2 : angle 2.34721 / 1.24 ( 12) link_ALPHA1-3 : bond 0.00266 / 0.16 ( 8) link_ALPHA1-3 : angle 1.69731 / 1.03 ( 24) link_ALPHA1-6 : bond 0.00226 / 0.13 ( 8) link_ALPHA1-6 : angle 1.55898 / 0.93 ( 24) link_BETA1-4 : bond 0.00413 / 0.25 ( 31) link_BETA1-4 : angle 1.71048 / 1.17 ( 93) link_BETA1-6 : bond 0.00823 / 0.41 ( 2) link_BETA1-6 : angle 1.06852 / 0.66 ( 6) link_NAG-ASN : bond 0.00405 / 0.24 ( 23) link_NAG-ASN : angle 2.46942 / 1.59 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8591 (ttt) REVERT: E 10 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8507 (mp0) REVERT: E 23 LYS cc_start: 0.8683 (tttp) cc_final: 0.8165 (tttp) REVERT: E 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8155 (tt0) REVERT: E 65 GLN cc_start: 0.8440 (tt0) cc_final: 0.7832 (mm-40) REVERT: E 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6702 (t0) REVERT: F 11 LEU cc_start: 0.8708 (tp) cc_final: 0.8433 (tt) REVERT: F 82 ASP cc_start: 0.8608 (m-30) cc_final: 0.8188 (m-30) REVERT: J 160 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8595 (ttt) REVERT: A 10 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8439 (tp30) REVERT: A 23 LYS cc_start: 0.8947 (tttp) cc_final: 0.8645 (tptt) REVERT: A 39 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: A 46 GLU cc_start: 0.8704 (tt0) cc_final: 0.8169 (tt0) REVERT: A 65 GLN cc_start: 0.8458 (tt0) cc_final: 0.7862 (mm-40) REVERT: A 73 ASP cc_start: 0.7408 (t0) cc_final: 0.6816 (t0) REVERT: A 107 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8842 (m-30) REVERT: D 11 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8422 (tt) REVERT: D 81 GLU cc_start: 0.8657 (pm20) cc_final: 0.8381 (pm20) REVERT: D 82 ASP cc_start: 0.8639 (m-30) cc_final: 0.8299 (m-30) REVERT: D 104 LYS cc_start: 0.8563 (tppt) cc_final: 0.8340 (tppt) REVERT: K 160 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8599 (ttt) REVERT: B 10 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8500 (mp0) REVERT: B 23 LYS cc_start: 0.8695 (tttp) cc_final: 0.8164 (tttp) REVERT: B 46 GLU cc_start: 0.8636 (tt0) cc_final: 0.8150 (tt0) REVERT: B 65 GLN cc_start: 0.8443 (tt0) cc_final: 0.7834 (mm-40) REVERT: B 73 ASP cc_start: 0.7338 (t0) cc_final: 0.6697 (t0) REVERT: H 11 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8439 (tt) REVERT: H 82 ASP cc_start: 0.8587 (m-30) cc_final: 0.8176 (m-30) REVERT: H 104 LYS cc_start: 0.8574 (tppt) cc_final: 0.8359 (tppt) REVERT: L 160 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8599 (ttt) REVERT: C 10 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8510 (mp0) REVERT: C 23 LYS cc_start: 0.8690 (tttp) cc_final: 0.8156 (tttp) REVERT: C 46 GLU cc_start: 0.8627 (tt0) cc_final: 0.8204 (tt0) REVERT: C 65 GLN cc_start: 0.8465 (tt0) cc_final: 0.7874 (mm-40) REVERT: C 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6702 (t0) REVERT: I 11 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (tt) REVERT: I 82 ASP cc_start: 0.8626 (m-30) cc_final: 0.8231 (m-30) REVERT: I 104 LYS cc_start: 0.8555 (tppt) cc_final: 0.8328 (tppt) outliers start: 55 outliers final: 14 residues processed: 248 average time/residue: 0.7139 time to fit residues: 196.4669 Evaluate side-chains 236 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN 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 50 ASP Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 243 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 8 optimal weight: 0.4980 chunk 155 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN F 6 GLN J 441 ASN A 39 GLN D 6 GLN D 32 ASN D 92 ASN K 441 ASN H 6 GLN 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 = 0.3521 r_free = 0.3521 target = 0.090156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058689 restraints weight = 39825.492| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.91 r_work: 0.2751 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20876 Z= 0.128 Angle : 0.640 9.358 28498 Z= 0.319 Chirality : 0.044 0.141 3292 Planarity : 0.004 0.045 3534 Dihedral : 4.937 23.565 2732 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 11.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2488 helix: -0.25 (1.04), residues: 24 sheet: 0.45 (0.16), residues: 1060 loop : -0.73 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 87 TYR 0.020 0.001 TYR F 49 PHE 0.012 0.002 PHE J 410 TRP 0.021 0.001 TRP K 178 HIS 0.003 0.001 HIS K 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20756) covalent geometry : angle 0.62307 / 0.32 (28182) SS BOND : bond 0.00226 / 0.11 ( 44) SS BOND : angle 0.78381 / 0.54 ( 88) hydrogen bonds : bond 0.03400 / 2.25 ( 624) hydrogen bonds : angle 5.76538 / 4.05 ( 1668) link_ALPHA1-2 : bond 0.00528 / 0.24 ( 4) link_ALPHA1-2 : angle 2.07393 / 1.10 ( 12) link_ALPHA1-3 : bond 0.00539 / 0.34 ( 8) link_ALPHA1-3 : angle 1.38662 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00369 / 0.22 ( 8) link_ALPHA1-6 : angle 1.45615 / 0.87 ( 24) link_BETA1-4 : bond 0.00465 / 0.28 ( 31) link_BETA1-4 : angle 1.46337 / 0.99 ( 93) link_BETA1-6 : bond 0.00698 / 0.35 ( 2) link_BETA1-6 : angle 1.08967 / 0.64 ( 6) link_NAG-ASN : bond 0.00309 / 0.17 ( 23) link_NAG-ASN : angle 2.13719 / 1.37 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.882 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: 0.8514 (mp0) REVERT: E 46 GLU cc_start: 0.8622 (tt0) cc_final: 0.8211 (tt0) REVERT: E 65 GLN cc_start: 0.8323 (tt0) cc_final: 0.7717 (mm-40) REVERT: E 73 ASP cc_start: 0.7330 (t0) cc_final: 0.6668 (t0) REVERT: F 11 LEU cc_start: 0.8656 (tp) cc_final: 0.8385 (tt) REVERT: F 82 ASP cc_start: 0.8503 (m-30) cc_final: 0.8043 (m-30) REVERT: A 10 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8444 (tp30) REVERT: A 23 LYS cc_start: 0.8935 (tttp) cc_final: 0.8602 (tptt) REVERT: A 39 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7286 (tp40) REVERT: A 46 GLU cc_start: 0.8613 (tt0) cc_final: 0.8136 (tt0) REVERT: A 65 GLN cc_start: 0.8302 (tt0) cc_final: 0.7729 (mm-40) REVERT: A 73 ASP cc_start: 0.7407 (t0) cc_final: 0.6798 (t0) REVERT: D 11 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8410 (tt) REVERT: D 70 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7736 (mm-30) REVERT: D 81 GLU cc_start: 0.8707 (pm20) cc_final: 0.8456 (pm20) REVERT: D 82 ASP cc_start: 0.8728 (m-30) cc_final: 0.7958 (m-30) REVERT: B 10 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8508 (mp0) REVERT: B 46 GLU cc_start: 0.8617 (tt0) cc_final: 0.8209 (tt0) REVERT: B 65 GLN cc_start: 0.8370 (tt0) cc_final: 0.7765 (mm-40) REVERT: B 73 ASP cc_start: 0.7327 (t0) cc_final: 0.6661 (t0) REVERT: H 11 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8421 (tt) REVERT: H 82 ASP cc_start: 0.8349 (m-30) cc_final: 0.7942 (m-30) REVERT: C 10 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8519 (mp0) REVERT: C 46 GLU cc_start: 0.8658 (tt0) cc_final: 0.8173 (tt0) REVERT: C 65 GLN cc_start: 0.8305 (tt0) cc_final: 0.7609 (mm-40) REVERT: C 73 ASP cc_start: 0.7335 (t0) cc_final: 0.6671 (t0) REVERT: I 11 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8412 (tt) REVERT: I 70 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7739 (mm-30) REVERT: I 82 ASP cc_start: 0.8495 (m-30) cc_final: 0.8019 (m-30) outliers start: 49 outliers final: 19 residues processed: 248 average time/residue: 0.7787 time to fit residues: 213.6217 Evaluate side-chains 236 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 35 SER 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 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN A 39 GLN D 6 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 ASN H 32 ASN H 92 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 441 ASN I 6 GLN I 32 ASN I 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.087881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056492 restraints weight = 40301.790| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.91 r_work: 0.2700 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 20876 Z= 0.284 Angle : 0.742 9.965 28498 Z= 0.369 Chirality : 0.048 0.140 3292 Planarity : 0.005 0.055 3534 Dihedral : 5.303 24.008 2732 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.06 % Favored : 95.78 % Rotamer: Outliers : 2.80 % Allowed : 12.57 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2488 helix: -0.22 (1.12), residues: 24 sheet: 0.42 (0.16), residues: 1048 loop : -0.93 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 63 TYR 0.021 0.002 TYR I 49 PHE 0.017 0.002 PHE L 410 TRP 0.019 0.002 TRP K 178 HIS 0.006 0.002 HIS L 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (20756) covalent geometry : angle 0.71954 / 0.36 (28182) SS BOND : bond 0.00358 / 0.19 ( 44) SS BOND : angle 1.33658 / 0.89 ( 88) hydrogen bonds : bond 0.04064 / 2.68 ( 624) hydrogen bonds : angle 5.88099 / 4.12 ( 1668) link_ALPHA1-2 : bond 0.00187 / 0.09 ( 4) link_ALPHA1-2 : angle 2.43612 / 1.30 ( 12) link_ALPHA1-3 : bond 0.00204 / 0.12 ( 8) link_ALPHA1-3 : angle 1.78685 / 1.09 ( 24) link_ALPHA1-6 : bond 0.00182 / 0.11 ( 8) link_ALPHA1-6 : angle 1.59986 / 0.95 ( 24) link_BETA1-4 : bond 0.00389 / 0.23 ( 31) link_BETA1-4 : angle 1.74863 / 1.21 ( 93) link_BETA1-6 : bond 0.00839 / 0.42 ( 2) link_BETA1-6 : angle 1.07868 / 0.67 ( 6) link_NAG-ASN : bond 0.00476 / 0.29 ( 23) link_NAG-ASN : angle 2.54589 / 1.63 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: E 10 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8539 (mp0) REVERT: E 23 LYS cc_start: 0.8894 (tttm) cc_final: 0.8577 (tttp) REVERT: E 46 GLU cc_start: 0.8685 (tt0) cc_final: 0.8138 (tt0) REVERT: E 65 GLN cc_start: 0.8542 (tt0) cc_final: 0.7952 (mm-40) REVERT: E 73 ASP cc_start: 0.7388 (t0) cc_final: 0.6768 (t0) REVERT: E 77 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7672 (p) REVERT: F 11 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 82 ASP cc_start: 0.8576 (m-30) cc_final: 0.8110 (m-30) REVERT: J 103 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: A 10 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8421 (tp30) REVERT: A 23 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8594 (tptt) REVERT: A 39 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7281 (tp40) REVERT: A 46 GLU cc_start: 0.8626 (tt0) cc_final: 0.8132 (tt0) REVERT: A 65 GLN cc_start: 0.8573 (tt0) cc_final: 0.7964 (mm-40) REVERT: A 73 ASP cc_start: 0.7489 (t0) cc_final: 0.6902 (t0) REVERT: D 11 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8414 (tt) REVERT: D 81 GLU cc_start: 0.8833 (pm20) cc_final: 0.8539 (pm20) REVERT: D 82 ASP cc_start: 0.8741 (m-30) cc_final: 0.7891 (m-30) REVERT: B 10 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8530 (mp0) REVERT: B 23 LYS cc_start: 0.8908 (tttm) cc_final: 0.8607 (tttp) REVERT: B 46 GLU cc_start: 0.8679 (tt0) cc_final: 0.8140 (tt0) REVERT: B 65 GLN cc_start: 0.8543 (tt0) cc_final: 0.7946 (mm-40) REVERT: B 73 ASP cc_start: 0.7387 (t0) cc_final: 0.6767 (t0) REVERT: B 77 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7684 (p) REVERT: H 11 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8421 (tt) REVERT: H 82 ASP cc_start: 0.8464 (m-30) cc_final: 0.8084 (m-30) REVERT: C 10 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8545 (mp0) REVERT: C 23 LYS cc_start: 0.8903 (tttm) cc_final: 0.8583 (tttp) REVERT: C 46 GLU cc_start: 0.8747 (tt0) cc_final: 0.8204 (tt0) REVERT: C 65 GLN cc_start: 0.8527 (tt0) cc_final: 0.7916 (mm-40) REVERT: C 73 ASP cc_start: 0.7375 (t0) cc_final: 0.6754 (t0) REVERT: C 77 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7673 (p) REVERT: I 11 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (tt) REVERT: I 82 ASP cc_start: 0.8548 (m-30) cc_final: 0.8094 (m-30) outliers start: 60 outliers final: 20 residues processed: 261 average time/residue: 0.7443 time to fit residues: 215.2767 Evaluate side-chains 242 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASP 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 35 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 103 ASP 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 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN 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 77 THR 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 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 115 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN D 6 GLN K 441 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 441 ASN I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058321 restraints weight = 39912.745| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.94 r_work: 0.2743 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20876 Z= 0.132 Angle : 0.668 10.821 28498 Z= 0.329 Chirality : 0.044 0.141 3292 Planarity : 0.005 0.053 3534 Dihedral : 4.984 23.608 2732 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.78 % Rotamer: Outliers : 2.20 % Allowed : 14.02 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2488 helix: -0.29 (1.03), residues: 24 sheet: 0.42 (0.16), residues: 1060 loop : -0.84 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 45 TYR 0.022 0.001 TYR D 49 PHE 0.013 0.002 PHE G 422 TRP 0.022 0.001 TRP K 178 HIS 0.003 0.001 HIS L 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20756) covalent geometry : angle 0.65208 / 0.33 (28182) SS BOND : bond 0.00268 / 0.14 ( 44) SS BOND : angle 0.94202 / 0.63 ( 88) hydrogen bonds : bond 0.03406 / 2.25 ( 624) hydrogen bonds : angle 5.67172 / 3.97 ( 1668) link_ALPHA1-2 : bond 0.00513 / 0.24 ( 4) link_ALPHA1-2 : angle 2.15822 / 1.15 ( 12) link_ALPHA1-3 : bond 0.00514 / 0.32 ( 8) link_ALPHA1-3 : angle 1.40111 / 0.86 ( 24) link_ALPHA1-6 : bond 0.00378 / 0.23 ( 8) link_ALPHA1-6 : angle 1.46157 / 0.88 ( 24) link_BETA1-4 : bond 0.00466 / 0.28 ( 31) link_BETA1-4 : angle 1.44609 / 0.98 ( 93) link_BETA1-6 : bond 0.00716 / 0.36 ( 2) link_BETA1-6 : angle 1.11125 / 0.65 ( 6) link_NAG-ASN : bond 0.00313 / 0.17 ( 23) link_NAG-ASN : angle 2.14082 / 1.38 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8560 (mp0) REVERT: E 23 LYS cc_start: 0.8908 (tttm) cc_final: 0.8577 (tttp) REVERT: E 46 GLU cc_start: 0.8621 (tt0) cc_final: 0.8048 (tt0) REVERT: E 65 GLN cc_start: 0.8385 (tt0) cc_final: 0.7856 (mm-40) REVERT: E 73 ASP cc_start: 0.7432 (t0) cc_final: 0.6810 (t0) REVERT: E 77 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7899 (p) REVERT: F 11 LEU cc_start: 0.8698 (tp) cc_final: 0.8418 (tt) REVERT: F 82 ASP cc_start: 0.8497 (m-30) cc_final: 0.8085 (m-30) REVERT: A 10 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8440 (tp30) REVERT: A 23 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8595 (tptt) REVERT: A 39 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7131 (tp40) REVERT: A 46 GLU cc_start: 0.8597 (tt0) cc_final: 0.8114 (tt0) REVERT: A 48 MET cc_start: 0.9214 (mtp) cc_final: 0.8999 (mtm) REVERT: A 65 GLN cc_start: 0.8418 (tt0) cc_final: 0.7894 (mm-40) REVERT: A 73 ASP cc_start: 0.7525 (t0) cc_final: 0.6942 (t0) REVERT: D 11 LEU cc_start: 0.8693 (tp) cc_final: 0.8426 (tt) REVERT: D 81 GLU cc_start: 0.8840 (pm20) cc_final: 0.8557 (pm20) REVERT: D 82 ASP cc_start: 0.8712 (m-30) cc_final: 0.7812 (m-30) REVERT: B 10 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8554 (mp0) REVERT: B 23 LYS cc_start: 0.8923 (tttm) cc_final: 0.8595 (tttp) REVERT: B 46 GLU cc_start: 0.8626 (tt0) cc_final: 0.8062 (tt0) REVERT: B 65 GLN cc_start: 0.8395 (tt0) cc_final: 0.7860 (mm-40) REVERT: B 73 ASP cc_start: 0.7444 (t0) cc_final: 0.6824 (t0) REVERT: B 77 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7904 (p) REVERT: H 11 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8425 (tt) REVERT: H 82 ASP cc_start: 0.8462 (m-30) cc_final: 0.7987 (m-30) REVERT: C 10 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8566 (mp0) REVERT: C 23 LYS cc_start: 0.8914 (tttm) cc_final: 0.8584 (tttp) REVERT: C 46 GLU cc_start: 0.8597 (tt0) cc_final: 0.8123 (tt0) REVERT: C 65 GLN cc_start: 0.8377 (tt0) cc_final: 0.7837 (mm-40) REVERT: C 73 ASP cc_start: 0.7421 (t0) cc_final: 0.6800 (t0) REVERT: C 77 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7899 (p) REVERT: I 6 GLN cc_start: 0.7716 (tt0) cc_final: 0.7262 (tt0) REVERT: I 11 LEU cc_start: 0.8693 (tp) cc_final: 0.8438 (tt) REVERT: I 82 ASP cc_start: 0.8500 (m-30) cc_final: 0.8085 (m-30) outliers start: 47 outliers final: 25 residues processed: 244 average time/residue: 0.7604 time to fit residues: 205.6636 Evaluate side-chains 236 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 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 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 51 ILE 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 K residue 467 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 11 LEU 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 L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 32 ASN F 92 ASN A 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.057556 restraints weight = 39873.601| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.89 r_work: 0.2728 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20876 Z= 0.193 Angle : 0.703 10.641 28498 Z= 0.346 Chirality : 0.046 0.139 3292 Planarity : 0.005 0.061 3534 Dihedral : 5.061 23.486 2732 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 2.48 % Allowed : 13.79 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2488 helix: -0.34 (1.05), residues: 24 sheet: 0.39 (0.16), residues: 1060 loop : -0.93 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 63 TYR 0.021 0.001 TYR H 49 PHE 0.014 0.002 PHE L 410 TRP 0.019 0.001 TRP K 178 HIS 0.004 0.001 HIS K 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (20756) covalent geometry : angle 0.68559 / 0.34 (28182) SS BOND : bond 0.00291 / 0.15 ( 44) SS BOND : angle 0.97029 / 0.65 ( 88) hydrogen bonds : bond 0.03619 / 2.39 ( 624) hydrogen bonds : angle 5.70841 / 4.00 ( 1668) link_ALPHA1-2 : bond 0.00377 / 0.17 ( 4) link_ALPHA1-2 : angle 2.24059 / 1.19 ( 12) link_ALPHA1-3 : bond 0.00333 / 0.20 ( 8) link_ALPHA1-3 : angle 1.54064 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00270 / 0.16 ( 8) link_ALPHA1-6 : angle 1.51669 / 0.91 ( 24) link_BETA1-4 : bond 0.00422 / 0.25 ( 31) link_BETA1-4 : angle 1.56017 / 1.07 ( 93) link_BETA1-6 : bond 0.00737 / 0.37 ( 2) link_BETA1-6 : angle 1.07841 / 0.65 ( 6) link_NAG-ASN : bond 0.00344 / 0.20 ( 23) link_NAG-ASN : angle 2.27515 / 1.46 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.538 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: E 10 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8557 (mp0) REVERT: E 23 LYS cc_start: 0.8903 (tttm) cc_final: 0.8600 (tttp) REVERT: E 46 GLU cc_start: 0.8684 (tt0) cc_final: 0.8147 (tt0) REVERT: E 65 GLN cc_start: 0.8556 (tt0) cc_final: 0.7975 (mm-40) REVERT: E 73 ASP cc_start: 0.7452 (t0) cc_final: 0.6839 (t0) REVERT: E 77 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7950 (p) REVERT: F 4 MET cc_start: 0.7861 (tpp) cc_final: 0.7466 (mmm) REVERT: F 11 LEU cc_start: 0.8647 (tp) cc_final: 0.8394 (tt) REVERT: F 82 ASP cc_start: 0.8497 (m-30) cc_final: 0.8101 (m-30) REVERT: A 10 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8422 (tp30) REVERT: A 39 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7095 (tp40) REVERT: A 46 GLU cc_start: 0.8631 (tt0) cc_final: 0.8004 (tt0) REVERT: A 48 MET cc_start: 0.9204 (mtp) cc_final: 0.8972 (mtm) REVERT: A 65 GLN cc_start: 0.8521 (tt0) cc_final: 0.7941 (mm-40) REVERT: A 73 ASP cc_start: 0.7537 (t0) cc_final: 0.6960 (t0) REVERT: D 4 MET cc_start: 0.7891 (tpp) cc_final: 0.7511 (mmm) REVERT: D 11 LEU cc_start: 0.8644 (tp) cc_final: 0.8375 (tt) REVERT: D 18 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8703 (tpp80) REVERT: D 81 GLU cc_start: 0.8828 (pm20) cc_final: 0.8535 (pm20) REVERT: D 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.7905 (m-30) REVERT: B 10 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8533 (mp0) REVERT: B 23 LYS cc_start: 0.8904 (tttm) cc_final: 0.8587 (tttp) REVERT: B 46 GLU cc_start: 0.8684 (tt0) cc_final: 0.8142 (tt0) REVERT: B 65 GLN cc_start: 0.8563 (tt0) cc_final: 0.7961 (mm-40) REVERT: B 73 ASP cc_start: 0.7459 (t0) cc_final: 0.6846 (t0) REVERT: B 77 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7946 (p) REVERT: B 87 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6599 (ptp-110) REVERT: B 90 ASP cc_start: 0.7850 (m-30) cc_final: 0.7577 (m-30) REVERT: H 4 MET cc_start: 0.7883 (tpp) cc_final: 0.7489 (mmm) REVERT: H 18 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8726 (tpp80) REVERT: H 82 ASP cc_start: 0.8516 (m-30) cc_final: 0.8262 (m-30) REVERT: C 10 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8545 (mp0) REVERT: C 23 LYS cc_start: 0.8905 (tttm) cc_final: 0.8591 (tttp) REVERT: C 46 GLU cc_start: 0.8715 (tt0) cc_final: 0.8142 (tt0) REVERT: C 65 GLN cc_start: 0.8477 (tt0) cc_final: 0.7914 (mm-40) REVERT: C 73 ASP cc_start: 0.7444 (t0) cc_final: 0.6830 (t0) REVERT: C 77 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7944 (p) REVERT: I 4 MET cc_start: 0.7836 (tpp) cc_final: 0.7447 (mmm) REVERT: I 6 GLN cc_start: 0.7925 (tt0) cc_final: 0.7695 (tt0) REVERT: I 11 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (tt) REVERT: I 82 ASP cc_start: 0.8531 (m-30) cc_final: 0.8128 (m-30) outliers start: 53 outliers final: 24 residues processed: 249 average time/residue: 0.6881 time to fit residues: 189.7790 Evaluate side-chains 235 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 39 GLN 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 35 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 11 LEU 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 19 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 198 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058217 restraints weight = 40057.503| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.91 r_work: 0.2746 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.003 0.043 20876 Z= 0.143 Angle : 0.683 10.924 28498 Z= 0.332 Chirality : 0.045 0.184 3292 Planarity : 0.005 0.057 3534 Dihedral : 4.887 23.261 2732 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 1.59 % Allowed : 14.77 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2488 helix: -0.32 (1.02), residues: 24 sheet: 0.44 (0.16), residues: 1060 loop : -0.88 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 45 TYR 0.021 0.001 TYR D 49 PHE 0.013 0.002 PHE K 422 TRP 0.021 0.001 TRP K 178 HIS 0.003 0.001 HIS K 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (20756) covalent geometry : angle 0.66730 / 0.33 (28182) SS BOND : bond 0.00258 / 0.14 ( 44) SS BOND : angle 0.85291 / 0.57 ( 88) hydrogen bonds : bond 0.03353 / 2.21 ( 624) hydrogen bonds : angle 5.61503 / 3.93 ( 1668) link_ALPHA1-2 : bond 0.00480 / 0.22 ( 4) link_ALPHA1-2 : angle 2.13767 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00448 / 0.28 ( 8) link_ALPHA1-3 : angle 1.41746 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00368 / 0.23 ( 8) link_ALPHA1-6 : angle 1.48964 / 0.89 ( 24) link_BETA1-4 : bond 0.00443 / 0.27 ( 31) link_BETA1-4 : angle 1.44474 / 0.98 ( 93) link_BETA1-6 : bond 0.00613 / 0.31 ( 2) link_BETA1-6 : angle 1.05424 / 0.62 ( 6) link_NAG-ASN : bond 0.00298 / 0.17 ( 23) link_NAG-ASN : angle 2.11301 / 1.36 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8545 (mp0) REVERT: E 23 LYS cc_start: 0.8918 (tttm) cc_final: 0.8607 (tttp) REVERT: E 46 GLU cc_start: 0.8700 (tt0) cc_final: 0.8107 (tt0) REVERT: E 65 GLN cc_start: 0.8486 (tt0) cc_final: 0.7941 (mm-40) REVERT: E 73 ASP cc_start: 0.7491 (t0) cc_final: 0.6846 (t0) REVERT: E 77 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (p) REVERT: E 98 ARG cc_start: 0.8828 (ptp-110) cc_final: 0.8551 (ptm160) REVERT: F 4 MET cc_start: 0.7830 (tpp) cc_final: 0.7528 (mmm) REVERT: F 11 LEU cc_start: 0.8664 (tp) cc_final: 0.8396 (tt) REVERT: F 18 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8678 (tpp80) REVERT: F 79 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8281 (mp-120) REVERT: F 82 ASP cc_start: 0.8503 (m-30) cc_final: 0.8034 (m-30) REVERT: A 10 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8395 (tp30) REVERT: A 23 LYS cc_start: 0.8955 (tttp) cc_final: 0.8697 (tttp) REVERT: A 39 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7076 (tp40) REVERT: A 46 GLU cc_start: 0.8549 (tt0) cc_final: 0.8144 (tt0) REVERT: A 65 GLN cc_start: 0.8475 (tt0) cc_final: 0.7947 (mm-40) REVERT: A 73 ASP cc_start: 0.7560 (t0) cc_final: 0.6956 (t0) REVERT: D 4 MET cc_start: 0.7825 (tpp) cc_final: 0.7564 (mmm) REVERT: D 18 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8777 (tpp80) REVERT: D 79 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7959 (mm110) REVERT: D 81 GLU cc_start: 0.8808 (pm20) cc_final: 0.8516 (pm20) REVERT: D 82 ASP cc_start: 0.8743 (m-30) cc_final: 0.7874 (m-30) REVERT: B 10 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8548 (mp0) REVERT: B 23 LYS cc_start: 0.8929 (tttm) cc_final: 0.8620 (tttp) REVERT: B 46 GLU cc_start: 0.8699 (tt0) cc_final: 0.8178 (tt0) REVERT: B 65 GLN cc_start: 0.8496 (tt0) cc_final: 0.7948 (mm-40) REVERT: B 73 ASP cc_start: 0.7495 (t0) cc_final: 0.6880 (t0) REVERT: B 77 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 98 ARG cc_start: 0.8830 (ptp-110) cc_final: 0.8553 (ptm160) REVERT: H 4 MET cc_start: 0.7836 (tpp) cc_final: 0.7537 (mmm) REVERT: H 18 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8837 (tpp80) REVERT: H 82 ASP cc_start: 0.8600 (m-30) cc_final: 0.8237 (m-30) REVERT: C 10 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8552 (mp0) REVERT: C 23 LYS cc_start: 0.8926 (tttm) cc_final: 0.8599 (tttp) REVERT: C 46 GLU cc_start: 0.8667 (tt0) cc_final: 0.8128 (tt0) REVERT: C 65 GLN cc_start: 0.8448 (tt0) cc_final: 0.7901 (mm-40) REVERT: C 73 ASP cc_start: 0.7485 (t0) cc_final: 0.6870 (t0) REVERT: C 77 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7991 (p) REVERT: C 98 ARG cc_start: 0.8831 (ptp-110) cc_final: 0.8552 (ptm160) REVERT: I 4 MET cc_start: 0.7831 (tpp) cc_final: 0.7556 (mmm) REVERT: I 11 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8428 (tt) REVERT: I 18 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8683 (tpp80) REVERT: I 82 ASP cc_start: 0.8535 (m-30) cc_final: 0.8078 (m-30) outliers start: 34 outliers final: 26 residues processed: 239 average time/residue: 0.7326 time to fit residues: 193.8126 Evaluate side-chains 242 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain 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 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 11 LEU 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 17 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN A 39 GLN K 441 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 441 ASN I 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056042 restraints weight = 40209.506| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.88 r_work: 0.2705 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 20876 Z= 0.285 Angle : 0.767 11.152 28498 Z= 0.377 Chirality : 0.048 0.137 3292 Planarity : 0.005 0.064 3534 Dihedral : 5.265 23.651 2732 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 1.59 % Allowed : 14.77 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2488 helix: -0.34 (1.09), residues: 24 sheet: 0.32 (0.16), residues: 1060 loop : -1.11 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 63 TYR 0.025 0.002 TYR H 49 PHE 0.018 0.002 PHE K 410 TRP 0.016 0.002 TRP G 178 HIS 0.005 0.001 HIS J 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (20756) covalent geometry : angle 0.74689 / 0.37 (28182) SS BOND : bond 0.00347 / 0.18 ( 44) SS BOND : angle 1.12335 / 0.75 ( 88) hydrogen bonds : bond 0.04046 / 2.67 ( 624) hydrogen bonds : angle 5.84651 / 4.09 ( 1668) link_ALPHA1-2 : bond 0.00189 / 0.09 ( 4) link_ALPHA1-2 : angle 2.43369 / 1.30 ( 12) link_ALPHA1-3 : bond 0.00202 / 0.12 ( 8) link_ALPHA1-3 : angle 1.77284 / 1.08 ( 24) link_ALPHA1-6 : bond 0.00166 / 0.10 ( 8) link_ALPHA1-6 : angle 1.59193 / 0.95 ( 24) link_BETA1-4 : bond 0.00373 / 0.22 ( 31) link_BETA1-4 : angle 1.72100 / 1.19 ( 93) link_BETA1-6 : bond 0.00769 / 0.39 ( 2) link_BETA1-6 : angle 1.05823 / 0.66 ( 6) link_NAG-ASN : bond 0.00497 / 0.30 ( 23) link_NAG-ASN : angle 2.52333 / 1.62 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.35 seconds wall clock time: 135 minutes 5.88 seconds (8105.88 seconds total)