Starting phenix.real_space_refine on Fri Aug 7 08:42:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3p_29707/08_2026/8g3p_29707.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12560 2.51 5 N 3448 2.21 5 O 4192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 40 Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "E" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: "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: 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: "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: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: "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: 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: "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: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: "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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.21 Number of scatterers: 20321 At special positions: 0 Unit cell: (166.83, 166.83, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4192 8.00 N 3448 7.00 C 12560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.08 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.06 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=1.99 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.07 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.09 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.09 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.14 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.08 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.06 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=1.99 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.07 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.07 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.09 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.07 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.09 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.08 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=1.99 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.07 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.07 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.09 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.07 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.09 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.08 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.06 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.99 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.07 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.09 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.07 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.09 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.14 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG M 1 " - " ASN A 86 " " NAG N 1 " - " ASN D 86 " " NAG O 1 " - " ASN E 86 " " NAG P 1 " - " ASN A 146 " " NAG Q 1 " - " ASN D 146 " " NAG R 1 " - " ASN E 146 " " NAG S 1 " - " ASN A 200 " " NAG T 1 " - " ASN D 200 " " NAG U 1 " - " ASN E 200 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN A 245 " " NAG Z 1 " - " ASN D 245 " " NAG a 1 " - " ASN E 245 " " NAG b 1 " - " ASN A 367 " " NAG c 1 " - " ASN D 367 " " NAG d 1 " - " ASN E 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 795.3 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: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.747A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.738A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.741A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.737A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.624A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.786A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU F 10 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 117 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.570A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.558A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.788A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP A 197 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.489A pdb=" N GLU G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.613A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.808A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 179 through 184 removed outlier: 4.048A pdb=" N ASP D 197 " --> pdb=" O ASN D 200 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.453A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 15.692A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.480A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.621A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.807A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.787A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.047A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.454A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.401A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.571A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 363 " --> pdb=" O TRP E 352 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.693A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.303A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3493 1.32 - 1.44: 5751 1.44 - 1.57: 11360 1.57 - 1.69: 4 1.69 - 1.82: 144 Bond restraints: 20752 Sorted by residual: bond pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" N ILE E 176 " pdb=" CA ILE E 176 " ideal model delta sigma weight residual 1.460 1.507 -0.048 1.10e-02 8.26e+03 1.89e+01 bond pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C GLU B 162 " pdb=" O GLU B 162 " ideal model delta sigma weight residual 1.234 1.283 -0.049 1.24e-02 6.50e+03 1.59e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21327 1.82 - 3.64: 5946 3.64 - 5.46: 766 5.46 - 7.28: 113 7.28 - 9.11: 16 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.29 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N ILE D 397 " pdb=" CA ILE D 397 " pdb=" C ILE D 397 " ideal model delta sigma weight residual 111.67 106.32 5.35 9.50e-01 1.11e+00 3.17e+01 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 111.67 106.35 5.32 9.50e-01 1.11e+00 3.14e+01 angle pdb=" CA ASP B 125 " pdb=" CB ASP B 125 " pdb=" CG ASP B 125 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.91e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10866 17.65 - 35.29: 620 35.29 - 52.94: 130 52.94 - 70.59: 48 70.59 - 88.24: 32 Dihedral angle restraints: 11696 sinusoidal: 4560 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASN E 441 " pdb=" C ASN E 441 " pdb=" N SER E 442 " pdb=" CA SER E 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN B 441 " pdb=" C ASN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASN D 441 " pdb=" C ASN D 441 " pdb=" N SER D 442 " pdb=" CA SER D 442 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 11693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2162 0.091 - 0.182: 1018 0.182 - 0.273: 92 0.273 - 0.364: 8 0.364 - 0.454: 12 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.79e+01 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.64e+01 ... (remaining 3289 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 281 " -0.084 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR D 281 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 281 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR D 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR D 281 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 281 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 281 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 281 " 0.085 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" CG TYR B 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 281 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.085 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR E 281 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4924 2.83 - 3.35: 19156 3.35 - 3.87: 36030 3.87 - 4.38: 44702 4.38 - 4.90: 72604 Nonbonded interactions: 177416 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP B 293 " pdb="CA CA B2000 " model vdw 2.314 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D2000 " model vdw 2.316 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.316 2.510 nonbonded pdb=" O HIS D 347 " pdb="CA CA D2000 " model vdw 2.317 2.510 ... (remaining 177411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 82 through 501) selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9376 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.107 20872 Z= 1.012 Angle : 1.682 12.309 28484 Z= 1.066 Chirality : 0.094 0.454 3292 Planarity : 0.010 0.071 3528 Dihedral : 13.509 88.236 7020 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2488 helix: -0.11 (0.97), residues: 24 sheet: -0.04 (0.16), residues: 1008 loop : -0.81 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG E 224 TYR 0.085 0.013 TYR B 281 PHE 0.060 0.013 PHE E 205 TRP 0.056 0.012 TRP J 97 HIS 0.021 0.006 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01455 / 1.01 (20752) covalent geometry : angle 1.63736 / 1.06 (28168) SS BOND : bond 0.05062 / 3.60 ( 44) SS BOND : angle 2.33670 / 1.71 ( 88) hydrogen bonds : bond 0.15070 / 10.58 ( 640) hydrogen bonds : angle 8.49030 / 5.84 ( 1680) link_ALPHA1-2 : bond 0.00807 / 0.40 ( 4) link_ALPHA1-2 : angle 4.60407 / 2.78 ( 12) link_ALPHA1-3 : bond 0.00989 / 0.47 ( 8) link_ALPHA1-3 : angle 2.54638 / 1.74 ( 24) link_ALPHA1-6 : bond 0.01189 / 0.58 ( 8) link_ALPHA1-6 : angle 2.42299 / 1.69 ( 24) link_BETA1-4 : bond 0.01430 / 1.06 ( 28) link_BETA1-4 : angle 4.56298 / 3.21 ( 84) link_BETA1-6 : bond 0.01042 / 0.53 ( 4) link_BETA1-6 : angle 3.14322 / 1.89 ( 12) link_NAG-ASN : bond 0.01036 / 0.68 ( 24) link_NAG-ASN : angle 5.47149 / 3.83 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.9335 (ttmt) cc_final: 0.9135 (mtpm) REVERT: I 70 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 400 ARG cc_start: 0.9264 (ptm-80) cc_final: 0.9027 (ptm160) REVERT: F 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: J 70 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9029 (ptm160) REVERT: G 23 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9133 (mtpm) REVERT: K 70 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 400 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.9028 (ptm160) REVERT: H 23 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9132 (mtpm) REVERT: L 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7811 (mt-10) REVERT: E 400 ARG cc_start: 0.9265 (ptm-80) cc_final: 0.9026 (ptm160) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.6692 time to fit residues: 216.0061 Evaluate side-chains 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 GLN C 65 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS F 32 GLN F 65 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS G 32 GLN G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS H 32 GLN H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055364 restraints weight = 37405.013| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.62 r_work: 0.2628 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20872 Z= 0.145 Angle : 0.697 8.268 28484 Z= 0.363 Chirality : 0.046 0.266 3292 Planarity : 0.004 0.047 3528 Dihedral : 6.266 24.198 2728 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 1.69 % Allowed : 6.79 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2488 helix: 0.19 (0.90), residues: 24 sheet: -0.08 (0.15), residues: 1072 loop : -0.24 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 45 TYR 0.014 0.002 TYR C 95 PHE 0.015 0.002 PHE D 410 TRP 0.022 0.002 TRP E 178 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (20752) covalent geometry : angle 0.67055 / 0.36 (28168) SS BOND : bond 0.00291 / 0.22 ( 44) SS BOND : angle 0.55943 / 0.41 ( 88) hydrogen bonds : bond 0.04675 / 3.21 ( 640) hydrogen bonds : angle 7.10678 / 4.90 ( 1680) link_ALPHA1-2 : bond 0.00874 / 0.44 ( 4) link_ALPHA1-2 : angle 1.73466 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00868 / 0.47 ( 8) link_ALPHA1-3 : angle 1.38431 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00546 / 0.28 ( 8) link_ALPHA1-6 : angle 1.25286 / 0.81 ( 24) link_BETA1-4 : bond 0.00412 / 0.29 ( 28) link_BETA1-4 : angle 2.10778 / 1.47 ( 84) link_BETA1-6 : bond 0.00628 / 0.32 ( 4) link_BETA1-6 : angle 1.28204 / 0.82 ( 12) link_NAG-ASN : bond 0.00302 / 0.22 ( 24) link_NAG-ASN : angle 2.92604 / 2.12 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.730 Fit side-chains REVERT: C 23 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8515 (mtpm) REVERT: I 17 GLU cc_start: 0.7710 (mp0) cc_final: 0.7437 (mp0) REVERT: I 24 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7142 (ttm110) REVERT: I 61 ARG cc_start: 0.8390 (ptm-80) cc_final: 0.7345 (ptm-80) REVERT: I 79 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7546 (mp-120) REVERT: I 81 GLU cc_start: 0.8889 (pm20) cc_final: 0.8635 (pp20) REVERT: B 400 ARG cc_start: 0.8616 (ptm-80) cc_final: 0.8315 (ptm160) REVERT: F 23 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8516 (mtpm) REVERT: J 17 GLU cc_start: 0.7707 (mp0) cc_final: 0.7430 (mp0) REVERT: J 24 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7184 (ttm110) REVERT: J 61 ARG cc_start: 0.8391 (ptm-80) cc_final: 0.7339 (ptm-80) REVERT: J 79 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7558 (mp-120) REVERT: J 81 GLU cc_start: 0.8892 (pm20) cc_final: 0.8637 (pp20) REVERT: A 400 ARG cc_start: 0.8616 (ptm-80) cc_final: 0.8317 (ptm160) REVERT: G 23 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8510 (mtpm) REVERT: K 17 GLU cc_start: 0.7702 (mp0) cc_final: 0.7429 (mp0) REVERT: K 24 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7148 (ttm110) REVERT: K 61 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: K 79 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7551 (mp-120) REVERT: K 81 GLU cc_start: 0.8887 (pm20) cc_final: 0.8637 (pp20) REVERT: D 400 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8325 (ptm160) REVERT: H 23 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8520 (mtpm) REVERT: L 17 GLU cc_start: 0.7704 (mp0) cc_final: 0.7431 (mp0) REVERT: L 24 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7142 (ttm110) REVERT: L 61 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.7351 (ptm-80) REVERT: L 79 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7553 (mp-120) REVERT: L 81 GLU cc_start: 0.8886 (pm20) cc_final: 0.8637 (pp20) REVERT: E 400 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8314 (ptm160) outliers start: 36 outliers final: 12 residues processed: 247 average time/residue: 0.7444 time to fit residues: 204.3138 Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS G 65 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS H 65 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.055896 restraints weight = 37743.550| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.61 r_work: 0.2644 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20872 Z= 0.130 Angle : 0.617 6.772 28484 Z= 0.323 Chirality : 0.045 0.236 3292 Planarity : 0.003 0.028 3528 Dihedral : 5.529 21.532 2728 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 8.61 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2488 helix: -0.23 (0.79), residues: 24 sheet: -0.07 (0.15), residues: 1068 loop : -0.16 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 45 TYR 0.014 0.001 TYR D 121 PHE 0.014 0.002 PHE A 410 TRP 0.017 0.001 TRP D 178 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (20752) covalent geometry : angle 0.59655 / 0.32 (28168) SS BOND : bond 0.00223 / 0.16 ( 44) SS BOND : angle 0.41897 / 0.32 ( 88) hydrogen bonds : bond 0.04086 / 2.83 ( 640) hydrogen bonds : angle 6.65246 / 4.58 ( 1680) link_ALPHA1-2 : bond 0.00907 / 0.46 ( 4) link_ALPHA1-2 : angle 1.80895 / 1.11 ( 12) link_ALPHA1-3 : bond 0.00533 / 0.28 ( 8) link_ALPHA1-3 : angle 1.21309 / 0.80 ( 24) link_ALPHA1-6 : bond 0.00529 / 0.28 ( 8) link_ALPHA1-6 : angle 1.38253 / 0.91 ( 24) link_BETA1-4 : bond 0.00454 / 0.32 ( 28) link_BETA1-4 : angle 1.72476 / 1.20 ( 84) link_BETA1-6 : bond 0.00464 / 0.24 ( 4) link_BETA1-6 : angle 1.65191 / 1.05 ( 12) link_NAG-ASN : bond 0.00165 / 0.10 ( 24) link_NAG-ASN : angle 2.37796 / 1.75 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8451 (mtpm) REVERT: I 17 GLU cc_start: 0.7834 (mp0) cc_final: 0.7539 (mp0) REVERT: I 24 ARG cc_start: 0.7659 (ttm110) cc_final: 0.6917 (ttm110) REVERT: I 61 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.7969 (ptm-80) REVERT: I 81 GLU cc_start: 0.8905 (pm20) cc_final: 0.8616 (pp20) REVERT: I 107 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.6963 (mm) REVERT: B 400 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8296 (ptm160) REVERT: F 23 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8446 (mtpm) REVERT: J 17 GLU cc_start: 0.7810 (mp0) cc_final: 0.7508 (mp0) REVERT: J 24 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7075 (ttm110) REVERT: J 61 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8051 (ptm-80) REVERT: J 81 GLU cc_start: 0.8902 (pm20) cc_final: 0.8621 (pp20) REVERT: J 107 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.6943 (mm) REVERT: A 400 ARG cc_start: 0.8618 (ptm-80) cc_final: 0.8291 (ptm160) REVERT: G 23 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8446 (mtpm) REVERT: G 46 GLU cc_start: 0.8013 (tt0) cc_final: 0.7741 (tt0) REVERT: K 17 GLU cc_start: 0.7831 (mp0) cc_final: 0.7535 (mp0) REVERT: K 24 ARG cc_start: 0.7640 (ttm110) cc_final: 0.6906 (ttm110) REVERT: K 61 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.8036 (ptm-80) REVERT: K 81 GLU cc_start: 0.8909 (pm20) cc_final: 0.8619 (pp20) REVERT: K 107 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6932 (mm) REVERT: D 400 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8296 (ptm160) REVERT: H 23 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8421 (mtpm) REVERT: H 90 ASP cc_start: 0.7615 (m-30) cc_final: 0.7125 (m-30) REVERT: L 17 GLU cc_start: 0.7833 (mp0) cc_final: 0.7537 (mp0) REVERT: L 24 ARG cc_start: 0.7644 (ttm110) cc_final: 0.6906 (ttm110) REVERT: L 61 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8057 (ptm-80) REVERT: L 81 GLU cc_start: 0.8906 (pm20) cc_final: 0.8622 (pp20) REVERT: L 107 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.6936 (mm) REVERT: E 400 ARG cc_start: 0.8613 (ptm-80) cc_final: 0.8286 (ptm160) outliers start: 30 outliers final: 16 residues processed: 236 average time/residue: 0.7706 time to fit residues: 200.4798 Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 GLN B 274 HIS B 468 HIS ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 468 HIS D 274 HIS D 468 HIS E 274 HIS E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.053610 restraints weight = 38034.099| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.64 r_work: 0.2594 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20872 Z= 0.225 Angle : 0.658 6.763 28484 Z= 0.344 Chirality : 0.046 0.247 3292 Planarity : 0.004 0.040 3528 Dihedral : 5.529 21.631 2728 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer: Outliers : 1.64 % Allowed : 9.50 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2488 helix: -0.13 (0.77), residues: 24 sheet: -0.19 (0.15), residues: 1088 loop : -0.15 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 45 TYR 0.016 0.002 TYR E 121 PHE 0.014 0.002 PHE A 410 TRP 0.016 0.001 TRP A 178 HIS 0.003 0.001 HIS E 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (20752) covalent geometry : angle 0.63615 / 0.34 (28168) SS BOND : bond 0.00326 / 0.24 ( 44) SS BOND : angle 0.74855 / 0.56 ( 88) hydrogen bonds : bond 0.04440 / 3.07 ( 640) hydrogen bonds : angle 6.61043 / 4.55 ( 1680) link_ALPHA1-2 : bond 0.00412 / 0.21 ( 4) link_ALPHA1-2 : angle 1.86036 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00342 / 0.19 ( 8) link_ALPHA1-3 : angle 1.47691 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00307 / 0.15 ( 8) link_ALPHA1-6 : angle 1.43202 / 0.94 ( 24) link_BETA1-4 : bond 0.00289 / 0.21 ( 28) link_BETA1-4 : angle 1.81536 / 1.24 ( 84) link_BETA1-6 : bond 0.00103 / 0.05 ( 4) link_BETA1-6 : angle 1.66877 / 1.03 ( 12) link_NAG-ASN : bond 0.00267 / 0.17 ( 24) link_NAG-ASN : angle 2.48368 / 1.83 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.763 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: C 23 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8451 (mtpm) REVERT: C 46 GLU cc_start: 0.8065 (tt0) cc_final: 0.7653 (tt0) REVERT: C 63 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8124 (mtp-110) REVERT: C 111 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: I 17 GLU cc_start: 0.7881 (mp0) cc_final: 0.7560 (mp0) REVERT: I 24 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7329 (ttm110) REVERT: I 70 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6996 (mm-30) REVERT: I 81 GLU cc_start: 0.8869 (pm20) cc_final: 0.8626 (pp20) REVERT: I 107 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7010 (mm) REVERT: B 400 ARG cc_start: 0.8677 (ptm-80) cc_final: 0.8362 (ptm160) REVERT: F 23 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8447 (mtpm) REVERT: F 46 GLU cc_start: 0.8051 (tt0) cc_final: 0.7827 (tt0) REVERT: F 111 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: J 17 GLU cc_start: 0.7855 (mp0) cc_final: 0.7539 (mp0) REVERT: J 24 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7363 (ttm110) REVERT: J 70 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7003 (mm-30) REVERT: J 81 GLU cc_start: 0.8872 (pm20) cc_final: 0.8627 (pp20) REVERT: J 107 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7013 (mm) REVERT: A 400 ARG cc_start: 0.8674 (ptm-80) cc_final: 0.8357 (ptm160) REVERT: G 23 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8441 (mtpm) REVERT: G 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7774 (tt0) REVERT: G 63 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.8245 (mtp-110) REVERT: G 98 ARG cc_start: 0.8736 (ttp80) cc_final: 0.8451 (ttp80) REVERT: G 111 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: K 4 MET cc_start: 0.8520 (mmm) cc_final: 0.8305 (mmm) REVERT: K 17 GLU cc_start: 0.7879 (mp0) cc_final: 0.7557 (mp0) REVERT: K 24 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7380 (ttm110) REVERT: K 70 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7073 (mm-30) REVERT: K 81 GLU cc_start: 0.8868 (pm20) cc_final: 0.8625 (pp20) REVERT: K 107 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7009 (mm) REVERT: D 400 ARG cc_start: 0.8672 (ptm-80) cc_final: 0.8355 (ptm160) REVERT: H 23 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8447 (mtpm) REVERT: H 46 GLU cc_start: 0.8097 (tt0) cc_final: 0.7714 (tt0) REVERT: H 63 ARG cc_start: 0.8587 (mtp-110) cc_final: 0.8210 (mtp-110) REVERT: H 111 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: L 4 MET cc_start: 0.8525 (mmm) cc_final: 0.8307 (mmm) REVERT: L 17 GLU cc_start: 0.7879 (mp0) cc_final: 0.7560 (mp0) REVERT: L 24 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7331 (ttm110) REVERT: L 70 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7067 (mm-30) REVERT: L 81 GLU cc_start: 0.8873 (pm20) cc_final: 0.8629 (pp20) REVERT: L 107 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7013 (mm) REVERT: E 400 ARG cc_start: 0.8667 (ptm-80) cc_final: 0.8349 (ptm160) outliers start: 35 outliers final: 24 residues processed: 227 average time/residue: 0.7416 time to fit residues: 186.8025 Evaluate side-chains 230 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 GLN B 468 HIS F 32 GLN F 65 GLN A 468 HIS G 32 GLN D 468 HIS H 32 GLN E 441 ASN E 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.054036 restraints weight = 37871.727| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.64 r_work: 0.2606 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20872 Z= 0.186 Angle : 0.629 6.526 28484 Z= 0.327 Chirality : 0.045 0.240 3292 Planarity : 0.004 0.040 3528 Dihedral : 5.367 21.572 2728 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.54 % Allowed : 10.67 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2488 helix: -0.16 (0.76), residues: 24 sheet: -0.25 (0.15), residues: 1088 loop : -0.09 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 45 TYR 0.013 0.001 TYR A 121 PHE 0.014 0.002 PHE D 410 TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (20752) covalent geometry : angle 0.60829 / 0.32 (28168) SS BOND : bond 0.00281 / 0.21 ( 44) SS BOND : angle 0.59831 / 0.47 ( 88) hydrogen bonds : bond 0.04132 / 2.86 ( 640) hydrogen bonds : angle 6.40707 / 4.41 ( 1680) link_ALPHA1-2 : bond 0.00533 / 0.27 ( 4) link_ALPHA1-2 : angle 1.85204 / 1.13 ( 12) link_ALPHA1-3 : bond 0.00461 / 0.25 ( 8) link_ALPHA1-3 : angle 1.40929 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00348 / 0.17 ( 8) link_ALPHA1-6 : angle 1.41444 / 0.92 ( 24) link_BETA1-4 : bond 0.00300 / 0.22 ( 28) link_BETA1-4 : angle 1.68441 / 1.15 ( 84) link_BETA1-6 : bond 0.00071 / 0.03 ( 4) link_BETA1-6 : angle 1.60701 / 1.03 ( 12) link_NAG-ASN : bond 0.00221 / 0.14 ( 24) link_NAG-ASN : angle 2.33278 / 1.73 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.784 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: C 23 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8471 (mtpm) REVERT: C 46 GLU cc_start: 0.8107 (tt0) cc_final: 0.7869 (tt0) REVERT: I 17 GLU cc_start: 0.7905 (mp0) cc_final: 0.7567 (mp0) REVERT: I 24 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7615 (ttm110) REVERT: I 81 GLU cc_start: 0.8877 (pm20) cc_final: 0.8640 (pp20) REVERT: I 107 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.6953 (mm) REVERT: B 400 ARG cc_start: 0.8690 (ptm-80) cc_final: 0.8283 (ptm160) REVERT: F 23 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8441 (mtpm) REVERT: F 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7708 (tt0) REVERT: F 63 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8237 (mtp-110) REVERT: J 4 MET cc_start: 0.8617 (mmm) cc_final: 0.8309 (mmm) REVERT: J 17 GLU cc_start: 0.7906 (mp0) cc_final: 0.7632 (mp0) REVERT: J 24 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7612 (ttm110) REVERT: J 81 GLU cc_start: 0.8880 (pm20) cc_final: 0.8642 (pp20) REVERT: J 107 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.6963 (mm) REVERT: A 400 ARG cc_start: 0.8676 (ptm-80) cc_final: 0.8273 (ptm160) REVERT: G 23 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8446 (mtpm) REVERT: G 46 GLU cc_start: 0.8145 (tt0) cc_final: 0.7723 (tt0) REVERT: K 17 GLU cc_start: 0.7924 (mp0) cc_final: 0.7575 (mp0) REVERT: K 24 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7606 (ttm110) REVERT: K 81 GLU cc_start: 0.8877 (pm20) cc_final: 0.8639 (pp20) REVERT: K 107 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.6954 (mm) REVERT: D 400 ARG cc_start: 0.8683 (ptm-80) cc_final: 0.8275 (ptm160) REVERT: H 23 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8472 (mtpm) REVERT: H 46 GLU cc_start: 0.8065 (tt0) cc_final: 0.7846 (tt0) REVERT: L 17 GLU cc_start: 0.7884 (mp0) cc_final: 0.7525 (mp0) REVERT: L 24 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7607 (ttm110) REVERT: L 81 GLU cc_start: 0.8882 (pm20) cc_final: 0.8643 (pp20) REVERT: L 107 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.6960 (mm) REVERT: E 400 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.8265 (ptm160) outliers start: 33 outliers final: 24 residues processed: 213 average time/residue: 0.6892 time to fit residues: 164.0574 Evaluate side-chains 222 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 243 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 ASN B 468 HIS A 441 ASN A 468 HIS G 65 GLN D 441 ASN D 468 HIS H 65 GLN E 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.052937 restraints weight = 38078.982| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.64 r_work: 0.2578 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20872 Z= 0.250 Angle : 0.664 6.602 28484 Z= 0.345 Chirality : 0.046 0.225 3292 Planarity : 0.004 0.049 3528 Dihedral : 5.448 21.760 2728 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.54 % Allowed : 11.00 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2488 helix: -0.04 (0.77), residues: 24 sheet: -0.30 (0.15), residues: 1080 loop : -0.13 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 45 TYR 0.016 0.002 TYR D 121 PHE 0.015 0.002 PHE B 410 TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (20752) covalent geometry : angle 0.64307 / 0.34 (28168) SS BOND : bond 0.00355 / 0.26 ( 44) SS BOND : angle 0.69780 / 0.54 ( 88) hydrogen bonds : bond 0.04401 / 3.05 ( 640) hydrogen bonds : angle 6.43103 / 4.42 ( 1680) link_ALPHA1-2 : bond 0.00335 / 0.17 ( 4) link_ALPHA1-2 : angle 1.89395 / 1.16 ( 12) link_ALPHA1-3 : bond 0.00322 / 0.18 ( 8) link_ALPHA1-3 : angle 1.55924 / 1.02 ( 24) link_ALPHA1-6 : bond 0.00262 / 0.12 ( 8) link_ALPHA1-6 : angle 1.41721 / 0.93 ( 24) link_BETA1-4 : bond 0.00207 / 0.15 ( 28) link_BETA1-4 : angle 1.78711 / 1.21 ( 84) link_BETA1-6 : bond 0.00057 / 0.03 ( 4) link_BETA1-6 : angle 1.50515 / 0.94 ( 12) link_NAG-ASN : bond 0.00310 / 0.19 ( 24) link_NAG-ASN : angle 2.42883 / 1.80 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.529 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: C 23 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8565 (mtpm) REVERT: C 46 GLU cc_start: 0.8128 (tt0) cc_final: 0.7909 (tt0) REVERT: I 17 GLU cc_start: 0.7923 (mp0) cc_final: 0.7652 (mp0) REVERT: I 24 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7748 (ttm110) REVERT: I 81 GLU cc_start: 0.8853 (pm20) cc_final: 0.8608 (pp20) REVERT: I 107 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7212 (pp) REVERT: B 400 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8296 (ptm160) REVERT: F 23 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8555 (mtpm) REVERT: F 46 GLU cc_start: 0.8128 (tt0) cc_final: 0.7776 (tt0) REVERT: F 63 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8288 (mtp-110) REVERT: J 17 GLU cc_start: 0.7947 (mp0) cc_final: 0.7691 (mp0) REVERT: J 24 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7628 (ttm110) REVERT: J 70 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7208 (mm-30) REVERT: J 81 GLU cc_start: 0.8860 (pm20) cc_final: 0.8617 (pp20) REVERT: J 107 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7342 (pp) REVERT: A 400 ARG cc_start: 0.8713 (ptm-80) cc_final: 0.8326 (ptm160) REVERT: G 23 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8534 (mtpm) REVERT: G 46 GLU cc_start: 0.8212 (tt0) cc_final: 0.7746 (tt0) REVERT: K 17 GLU cc_start: 0.7939 (mp0) cc_final: 0.7688 (mp0) REVERT: K 24 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7742 (ttm110) REVERT: K 81 GLU cc_start: 0.8863 (pm20) cc_final: 0.8632 (pp20) REVERT: K 107 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7329 (pp) REVERT: D 400 ARG cc_start: 0.8721 (ptm-80) cc_final: 0.8284 (ptm160) REVERT: H 23 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8565 (mtpm) REVERT: H 46 GLU cc_start: 0.8106 (tt0) cc_final: 0.7890 (tt0) REVERT: L 17 GLU cc_start: 0.7930 (mp0) cc_final: 0.7680 (mp0) REVERT: L 24 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7734 (ttm110) REVERT: L 81 GLU cc_start: 0.8859 (pm20) cc_final: 0.8624 (pp20) REVERT: L 107 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7336 (pp) REVERT: E 400 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8281 (ptm160) outliers start: 33 outliers final: 25 residues processed: 216 average time/residue: 0.6194 time to fit residues: 150.0726 Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.054528 restraints weight = 38097.855| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.63 r_work: 0.2618 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20872 Z= 0.155 Angle : 0.622 7.027 28484 Z= 0.321 Chirality : 0.044 0.222 3292 Planarity : 0.004 0.047 3528 Dihedral : 5.192 21.543 2728 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Rotamer: Outliers : 1.26 % Allowed : 11.75 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2488 helix: -0.98 (0.74), residues: 28 sheet: -0.30 (0.15), residues: 1080 loop : -0.06 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 45 TYR 0.011 0.001 TYR A 121 PHE 0.014 0.002 PHE D 410 TRP 0.017 0.001 TRP D 178 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (20752) covalent geometry : angle 0.60460 / 0.32 (28168) SS BOND : bond 0.00240 / 0.18 ( 44) SS BOND : angle 0.53298 / 0.42 ( 88) hydrogen bonds : bond 0.03826 / 2.64 ( 640) hydrogen bonds : angle 6.21256 / 4.27 ( 1680) link_ALPHA1-2 : bond 0.00606 / 0.30 ( 4) link_ALPHA1-2 : angle 1.91245 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00518 / 0.27 ( 8) link_ALPHA1-3 : angle 1.33729 / 0.89 ( 24) link_ALPHA1-6 : bond 0.00389 / 0.20 ( 8) link_ALPHA1-6 : angle 1.39459 / 0.91 ( 24) link_BETA1-4 : bond 0.00293 / 0.21 ( 28) link_BETA1-4 : angle 1.57026 / 1.07 ( 84) link_BETA1-6 : bond 0.00107 / 0.05 ( 4) link_BETA1-6 : angle 1.36909 / 0.86 ( 12) link_NAG-ASN : bond 0.00166 / 0.11 ( 24) link_NAG-ASN : angle 2.16057 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8573 (mtpm) REVERT: I 17 GLU cc_start: 0.7987 (mp0) cc_final: 0.7726 (mp0) REVERT: I 24 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7701 (ttm110) REVERT: I 45 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.8331 (mtp-110) REVERT: I 54 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8334 (ttp80) REVERT: I 79 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7739 (mp-120) REVERT: I 81 GLU cc_start: 0.8846 (pm20) cc_final: 0.8643 (pp20) REVERT: I 107 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7378 (pp) REVERT: B 400 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8322 (ptm160) REVERT: F 23 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8520 (mtpm) REVERT: F 46 GLU cc_start: 0.8129 (tt0) cc_final: 0.7669 (tt0) REVERT: F 63 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8241 (mtp-110) REVERT: J 17 GLU cc_start: 0.7958 (mp0) cc_final: 0.7742 (mp0) REVERT: J 24 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7667 (ttm110) REVERT: J 45 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8395 (mtp-110) REVERT: J 54 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8331 (ttp80) REVERT: J 79 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7781 (mp-120) REVERT: J 81 GLU cc_start: 0.8848 (pm20) cc_final: 0.8631 (pp20) REVERT: J 107 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 400 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8266 (ptm160) REVERT: G 23 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8455 (mtpm) REVERT: G 46 GLU cc_start: 0.8204 (tt0) cc_final: 0.7748 (tt0) REVERT: K 4 MET cc_start: 0.8571 (mmm) cc_final: 0.7977 (mmm) REVERT: K 17 GLU cc_start: 0.7977 (mp0) cc_final: 0.7717 (mp0) REVERT: K 24 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7544 (ttm110) REVERT: K 45 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8381 (mtp-110) REVERT: K 54 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8330 (ttp80) REVERT: K 79 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7764 (mp-120) REVERT: K 81 GLU cc_start: 0.8848 (pm20) cc_final: 0.8629 (pp20) REVERT: K 107 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7364 (pp) REVERT: D 400 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8270 (ptm160) REVERT: H 23 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8470 (mtpm) REVERT: H 46 GLU cc_start: 0.8095 (tt0) cc_final: 0.7687 (tt0) REVERT: H 63 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8220 (mtp-110) REVERT: L 4 MET cc_start: 0.8576 (mmm) cc_final: 0.7993 (mmm) REVERT: L 17 GLU cc_start: 0.7978 (mp0) cc_final: 0.7714 (mp0) REVERT: L 24 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7551 (ttm110) REVERT: L 54 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8303 (ttp80) REVERT: L 79 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7765 (mp-120) REVERT: L 81 GLU cc_start: 0.8852 (pm20) cc_final: 0.8634 (pp20) REVERT: L 107 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7373 (pp) REVERT: E 400 ARG cc_start: 0.8694 (ptm-80) cc_final: 0.8309 (ptm160) outliers start: 27 outliers final: 19 residues processed: 211 average time/residue: 0.6085 time to fit residues: 143.8452 Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.052442 restraints weight = 38203.857| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.65 r_work: 0.2567 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20872 Z= 0.288 Angle : 0.692 6.788 28484 Z= 0.357 Chirality : 0.047 0.225 3292 Planarity : 0.004 0.054 3528 Dihedral : 5.429 21.866 2728 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 1.50 % Allowed : 11.99 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2488 helix: -0.06 (0.77), residues: 24 sheet: -0.36 (0.15), residues: 1080 loop : -0.20 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 18 TYR 0.016 0.002 TYR A 121 PHE 0.016 0.002 PHE A 410 TRP 0.017 0.002 TRP A 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.29 (20752) covalent geometry : angle 0.67079 / 0.35 (28168) SS BOND : bond 0.00403 / 0.30 ( 44) SS BOND : angle 0.76735 / 0.60 ( 88) hydrogen bonds : bond 0.04504 / 3.12 ( 640) hydrogen bonds : angle 6.41728 / 4.40 ( 1680) link_ALPHA1-2 : bond 0.00222 / 0.11 ( 4) link_ALPHA1-2 : angle 1.91173 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00240 / 0.13 ( 8) link_ALPHA1-3 : angle 1.62515 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00242 / 0.11 ( 8) link_ALPHA1-6 : angle 1.42144 / 0.93 ( 24) link_BETA1-4 : bond 0.00192 / 0.14 ( 28) link_BETA1-4 : angle 1.83708 / 1.24 ( 84) link_BETA1-6 : bond 0.00142 / 0.07 ( 4) link_BETA1-6 : angle 1.58277 / 0.98 ( 12) link_NAG-ASN : bond 0.00375 / 0.24 ( 24) link_NAG-ASN : angle 2.48401 / 1.84 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8556 (mtpm) REVERT: I 17 GLU cc_start: 0.7983 (mp0) cc_final: 0.7725 (mp0) REVERT: I 24 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7659 (ttm110) REVERT: I 70 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7270 (mm-30) REVERT: I 81 GLU cc_start: 0.8854 (pm20) cc_final: 0.8608 (pp20) REVERT: I 107 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7329 (pp) REVERT: B 400 ARG cc_start: 0.8747 (ptm-80) cc_final: 0.8336 (ptm160) REVERT: F 13 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8833 (mp0) REVERT: F 23 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8571 (mtpm) REVERT: F 63 ARG cc_start: 0.8636 (mtp-110) cc_final: 0.8293 (mtp-110) REVERT: J 17 GLU cc_start: 0.8034 (mp0) cc_final: 0.7659 (mp0) REVERT: J 24 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7716 (ttm110) REVERT: J 70 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7287 (mm-30) REVERT: J 81 GLU cc_start: 0.8851 (pm20) cc_final: 0.8603 (pp20) REVERT: J 107 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7338 (pp) REVERT: A 400 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8282 (ptm160) REVERT: G 23 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8547 (mtpm) REVERT: G 46 GLU cc_start: 0.8217 (tt0) cc_final: 0.7750 (tt0) REVERT: K 17 GLU cc_start: 0.7975 (mp0) cc_final: 0.7717 (mp0) REVERT: K 81 GLU cc_start: 0.8850 (pm20) cc_final: 0.8602 (pp20) REVERT: K 107 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7330 (pp) REVERT: D 400 ARG cc_start: 0.8745 (ptm-80) cc_final: 0.8292 (ptm160) REVERT: H 23 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8575 (mtpm) REVERT: H 46 GLU cc_start: 0.8123 (tt0) cc_final: 0.7915 (tt0) REVERT: L 17 GLU cc_start: 0.7972 (mp0) cc_final: 0.7715 (mp0) REVERT: L 45 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8383 (mtp-110) REVERT: L 81 GLU cc_start: 0.8852 (pm20) cc_final: 0.8607 (pp20) REVERT: L 107 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7335 (pp) REVERT: E 400 ARG cc_start: 0.8740 (ptm-80) cc_final: 0.8289 (ptm160) outliers start: 32 outliers final: 26 residues processed: 212 average time/residue: 0.6272 time to fit residues: 149.3318 Evaluate side-chains 223 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 187 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.052984 restraints weight = 38042.113| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.63 r_work: 0.2581 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20872 Z= 0.231 Angle : 0.671 7.426 28484 Z= 0.346 Chirality : 0.046 0.231 3292 Planarity : 0.004 0.059 3528 Dihedral : 5.379 21.824 2728 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.54 % Allowed : 12.22 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2488 helix: 0.03 (0.76), residues: 24 sheet: -0.38 (0.15), residues: 1080 loop : -0.20 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 45 TYR 0.014 0.002 TYR A 121 PHE 0.016 0.002 PHE B 410 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS B 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (20752) covalent geometry : angle 0.65107 / 0.34 (28168) SS BOND : bond 0.00317 / 0.23 ( 44) SS BOND : angle 0.65489 / 0.51 ( 88) hydrogen bonds : bond 0.04264 / 2.95 ( 640) hydrogen bonds : angle 6.35361 / 4.36 ( 1680) link_ALPHA1-2 : bond 0.00343 / 0.17 ( 4) link_ALPHA1-2 : angle 1.93426 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00363 / 0.19 ( 8) link_ALPHA1-3 : angle 1.51573 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00293 / 0.14 ( 8) link_ALPHA1-6 : angle 1.41334 / 0.92 ( 24) link_BETA1-4 : bond 0.00186 / 0.13 ( 28) link_BETA1-4 : angle 1.73207 / 1.17 ( 84) link_BETA1-6 : bond 0.00086 / 0.04 ( 4) link_BETA1-6 : angle 1.51621 / 0.95 ( 12) link_NAG-ASN : bond 0.00306 / 0.19 ( 24) link_NAG-ASN : angle 2.39145 / 1.77 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8842 (mp0) REVERT: C 23 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8569 (mtpm) REVERT: I 17 GLU cc_start: 0.7990 (mp0) cc_final: 0.7729 (mp0) REVERT: I 24 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7639 (ttm110) REVERT: I 45 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8412 (mtp-110) REVERT: I 70 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7368 (mm-30) REVERT: I 79 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7736 (mp-120) REVERT: I 81 GLU cc_start: 0.8821 (pm20) cc_final: 0.8574 (pp20) REVERT: I 107 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7393 (pp) REVERT: B 400 ARG cc_start: 0.8739 (ptm-80) cc_final: 0.8290 (ptm160) REVERT: F 13 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8839 (mp0) REVERT: F 23 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8566 (mtpm) REVERT: J 17 GLU cc_start: 0.8019 (mp0) cc_final: 0.7736 (mp0) REVERT: J 24 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7689 (ttm110) REVERT: J 45 ARG cc_start: 0.8587 (mtp-110) cc_final: 0.8380 (mtp-110) REVERT: J 70 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7356 (mm-30) REVERT: J 79 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7775 (mp-120) REVERT: J 81 GLU cc_start: 0.8817 (pm20) cc_final: 0.8567 (pp20) REVERT: J 107 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7396 (pp) REVERT: A 400 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8281 (ptm160) REVERT: G 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8833 (mp0) REVERT: G 23 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8568 (mtpm) REVERT: G 46 GLU cc_start: 0.8217 (tt0) cc_final: 0.7757 (tt0) REVERT: K 17 GLU cc_start: 0.7988 (mp0) cc_final: 0.7727 (mp0) REVERT: K 24 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7498 (ttm110) REVERT: K 45 ARG cc_start: 0.8587 (mtp-110) cc_final: 0.8378 (mtp-110) REVERT: K 79 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7722 (mp-120) REVERT: K 81 GLU cc_start: 0.8814 (pm20) cc_final: 0.8565 (pp20) REVERT: K 107 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7388 (pp) REVERT: D 400 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8287 (ptm160) REVERT: H 23 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8570 (mtpm) REVERT: H 46 GLU cc_start: 0.8125 (tt0) cc_final: 0.7917 (tt0) REVERT: L 17 GLU cc_start: 0.7978 (mp0) cc_final: 0.7718 (mp0) REVERT: L 24 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7506 (ttm110) REVERT: L 45 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8357 (mtp-110) REVERT: L 79 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7717 (mp-120) REVERT: L 81 GLU cc_start: 0.8820 (pm20) cc_final: 0.8569 (pp20) REVERT: L 107 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7392 (pp) REVERT: E 400 ARG cc_start: 0.8730 (ptm-80) cc_final: 0.8280 (ptm160) outliers start: 33 outliers final: 23 residues processed: 214 average time/residue: 0.6491 time to fit residues: 155.5981 Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.053715 restraints weight = 37946.057| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.63 r_work: 0.2599 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20872 Z= 0.178 Angle : 0.646 7.588 28484 Z= 0.333 Chirality : 0.045 0.235 3292 Planarity : 0.004 0.057 3528 Dihedral : 5.282 21.711 2728 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 1.59 % Allowed : 12.08 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2488 helix: -0.69 (0.76), residues: 28 sheet: -0.35 (0.15), residues: 1080 loop : -0.19 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 45 TYR 0.012 0.001 TYR A 121 PHE 0.015 0.002 PHE B 410 TRP 0.018 0.001 TRP D 178 HIS 0.004 0.001 HIS E 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (20752) covalent geometry : angle 0.62724 / 0.33 (28168) SS BOND : bond 0.00247 / 0.18 ( 44) SS BOND : angle 0.56986 / 0.45 ( 88) hydrogen bonds : bond 0.03993 / 2.76 ( 640) hydrogen bonds : angle 6.27248 / 4.30 ( 1680) link_ALPHA1-2 : bond 0.00459 / 0.23 ( 4) link_ALPHA1-2 : angle 1.91748 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00470 / 0.25 ( 8) link_ALPHA1-3 : angle 1.44560 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00342 / 0.17 ( 8) link_ALPHA1-6 : angle 1.40480 / 0.92 ( 24) link_BETA1-4 : bond 0.00242 / 0.17 ( 28) link_BETA1-4 : angle 1.63402 / 1.11 ( 84) link_BETA1-6 : bond 0.00017 / 0.01 ( 4) link_BETA1-6 : angle 1.44627 / 0.90 ( 12) link_NAG-ASN : bond 0.00240 / 0.16 ( 24) link_NAG-ASN : angle 2.29489 / 1.70 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8835 (mp0) REVERT: C 23 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8565 (mtpm) REVERT: I 17 GLU cc_start: 0.8001 (mp0) cc_final: 0.7731 (mp0) REVERT: I 24 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7599 (ttm110) REVERT: I 45 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8391 (mtp-110) REVERT: I 70 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7328 (mm-30) REVERT: I 79 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7750 (mp-120) REVERT: I 81 GLU cc_start: 0.8800 (pm20) cc_final: 0.8563 (pp20) REVERT: I 107 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7404 (pp) REVERT: B 400 ARG cc_start: 0.8725 (ptm-80) cc_final: 0.8321 (ptm160) REVERT: F 13 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8830 (mp0) REVERT: F 23 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8568 (mtpm) REVERT: J 17 GLU cc_start: 0.8047 (mp0) cc_final: 0.7763 (mp0) REVERT: J 24 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7640 (ttm110) REVERT: J 45 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8387 (mtp-110) REVERT: J 54 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8367 (ttp80) REVERT: J 70 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7363 (mm-30) REVERT: J 79 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7719 (mp-120) REVERT: J 81 GLU cc_start: 0.8799 (pm20) cc_final: 0.8557 (pp20) REVERT: J 107 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7407 (pp) REVERT: A 400 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8310 (ptm160) REVERT: G 13 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8833 (mp0) REVERT: G 23 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8572 (mtpm) REVERT: G 46 GLU cc_start: 0.8193 (tt0) cc_final: 0.7743 (tt0) REVERT: K 17 GLU cc_start: 0.7981 (mp0) cc_final: 0.7715 (mp0) REVERT: K 24 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7555 (ttm110) REVERT: K 45 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8380 (mtp-110) REVERT: K 81 GLU cc_start: 0.8803 (pm20) cc_final: 0.8555 (pp20) REVERT: K 107 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7399 (pp) REVERT: D 400 ARG cc_start: 0.8723 (ptm-80) cc_final: 0.8316 (ptm160) REVERT: H 23 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8574 (mtpm) REVERT: H 46 GLU cc_start: 0.8111 (tt0) cc_final: 0.7907 (tt0) REVERT: L 17 GLU cc_start: 0.7979 (mp0) cc_final: 0.7715 (mp0) REVERT: L 24 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7555 (ttm110) REVERT: L 81 GLU cc_start: 0.8805 (pm20) cc_final: 0.8560 (pp20) REVERT: L 107 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7405 (pp) REVERT: E 400 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8312 (ptm160) outliers start: 34 outliers final: 22 residues processed: 213 average time/residue: 0.6278 time to fit residues: 149.5792 Evaluate side-chains 218 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain E residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 234 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 468 HIS A 468 HIS D 468 HIS E 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.053956 restraints weight = 37909.324| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.62 r_work: 0.2605 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20872 Z= 0.183 Angle : 0.648 7.404 28484 Z= 0.334 Chirality : 0.045 0.230 3292 Planarity : 0.004 0.056 3528 Dihedral : 5.217 21.594 2728 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 1.73 % Allowed : 12.08 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2488 helix: -0.68 (0.75), residues: 28 sheet: -0.32 (0.15), residues: 1080 loop : -0.14 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 45 TYR 0.012 0.001 TYR A 121 PHE 0.014 0.002 PHE E 410 TRP 0.017 0.001 TRP D 178 HIS 0.004 0.001 HIS E 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (20752) covalent geometry : angle 0.63048 / 0.33 (28168) SS BOND : bond 0.00261 / 0.19 ( 44) SS BOND : angle 0.51531 / 0.41 ( 88) hydrogen bonds : bond 0.03937 / 2.72 ( 640) hydrogen bonds : angle 6.16788 / 4.23 ( 1680) link_ALPHA1-2 : bond 0.00440 / 0.22 ( 4) link_ALPHA1-2 : angle 1.85639 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00438 / 0.23 ( 8) link_ALPHA1-3 : angle 1.43683 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00323 / 0.16 ( 8) link_ALPHA1-6 : angle 1.39038 / 0.91 ( 24) link_BETA1-4 : bond 0.00224 / 0.16 ( 28) link_BETA1-4 : angle 1.60413 / 1.09 ( 84) link_BETA1-6 : bond 0.00014 / 0.01 ( 4) link_BETA1-6 : angle 1.42655 / 0.89 ( 12) link_NAG-ASN : bond 0.00234 / 0.15 ( 24) link_NAG-ASN : angle 2.22303 / 1.65 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7595.27 seconds wall clock time: 130 minutes 15.04 seconds (7815.04 seconds total)