Starting phenix.real_space_refine on Sat Jul 4 06:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3m_29704/07_2026/8g3m_29704.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11520 2.51 5 N 3120 2.21 5 O 3913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18667 Number of models: 1 Model: "" Number of chains: 38 Chain: "G" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.83, per 1000 atoms: 0.26 Number of scatterers: 18667 At special positions: 0 Unit cell: (148.648, 137.718, 112.579, 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 109 16.00 O 3913 8.00 N 3120 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.06 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.09 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.09 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.08 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.05 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.12 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.04 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.06 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.06 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.08 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.05 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.08 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.16 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.07 Simple disulfide: pdb=" SG CYS K 92 " - pdb=" SG CYS K 417 " distance=2.04 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 129 " distance=2.07 Simple disulfide: pdb=" SG CYS K 175 " - pdb=" SG CYS K 193 " distance=2.12 Simple disulfide: pdb=" SG CYS K 183 " - pdb=" SG CYS K 230 " distance=2.11 Simple disulfide: pdb=" SG CYS K 232 " - pdb=" SG CYS K 237 " distance=2.08 Simple disulfide: pdb=" SG CYS K 278 " - pdb=" SG CYS K 291 " distance=2.15 Simple disulfide: pdb=" SG CYS K 280 " - pdb=" SG CYS K 289 " distance=2.13 Simple disulfide: pdb=" SG CYS K 318 " - pdb=" SG CYS K 337 " distance=2.10 Simple disulfide: pdb=" SG CYS K 421 " - pdb=" SG CYS K 447 " distance=2.20 Simple disulfide: pdb=" SG CYS L 92 " - pdb=" SG CYS L 417 " distance=2.05 Simple disulfide: pdb=" SG CYS L 124 " - pdb=" SG CYS L 129 " distance=2.06 Simple disulfide: pdb=" SG CYS L 175 " - pdb=" SG CYS L 193 " distance=2.06 Simple disulfide: pdb=" SG CYS L 183 " - pdb=" SG CYS L 230 " distance=2.10 Simple disulfide: pdb=" SG CYS L 232 " - pdb=" SG CYS L 237 " distance=2.08 Simple disulfide: pdb=" SG CYS L 278 " - pdb=" SG CYS L 291 " distance=2.07 Simple disulfide: pdb=" SG CYS L 280 " - pdb=" SG CYS L 289 " distance=2.10 Simple disulfide: pdb=" SG CYS L 318 " - pdb=" SG CYS L 337 " distance=2.08 Simple disulfide: pdb=" SG CYS L 421 " - pdb=" SG CYS L 447 " distance=2.17 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=2.06 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 P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " 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 r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG V 1 " - " FUC V 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 4 " " NAG X 1 " - " FUC X 4 " " NAG t 1 " - " FUC t 4 " NAG-ASN " NAG M 1 " - " ASN J 86 " " NAG N 1 " - " ASN K 86 " " NAG O 1 " - " ASN L 86 " " NAG P 1 " - " ASN J 146 " " NAG Q 1 " - " ASN K 146 " " NAG R 1 " - " ASN L 146 " " NAG S 1 " - " ASN J 200 " " NAG T 1 " - " ASN K 200 " " NAG U 1 " - " ASN L 200 " " NAG V 1 " - " ASN J 234 " " NAG W 1 " - " ASN K 234 " " NAG X 1 " - " ASN L 234 " " NAG Y 1 " - " ASN J 329 " " NAG Z 1 " - " ASN K 329 " " NAG a 1 " - " ASN L 329 " " NAG b 1 " - " ASN J 367 " " NAG c 1 " - " ASN K 367 " " NAG d 1 " - " ASN L 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 778.2 milliseconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 40 sheets defined 4.1% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.562A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 removed outlier: 3.631A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.567A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.625A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.629A pdb=" N ALA K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.582A pdb=" N ASN K 146 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 200 Processing helix chain 'L' and resid 104 through 110 removed outlier: 3.619A pdb=" N ALA L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.575A pdb=" N ASN L 146 " --> pdb=" O VAL L 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.613A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.626A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 3.667A pdb=" N SER G 179 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.676A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.193A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.804A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.858A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.512A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.424A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.424A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.536A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.603A pdb=" N LEU F 13 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.632A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.791A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 179 through 184 removed outlier: 3.680A pdb=" N SER J 179 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.680A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.412A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.224A pdb=" N ASN J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.891A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.515A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.534A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.605A pdb=" N LEU D 13 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 96 through 102 removed outlier: 3.896A pdb=" N GLY K 96 " --> pdb=" O THR K 449 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL K 445 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS K 102 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE K 443 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG K 420 " --> pdb=" O GLY K 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 115 through 124 removed outlier: 4.753A pdb=" N TRP K 115 " --> pdb=" O THR K 138 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR K 138 " --> pdb=" O TRP K 115 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR K 157 " --> pdb=" O GLY K 135 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU K 158 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 172 " --> pdb=" O MET K 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 179 through 184 removed outlier: 3.570A pdb=" N SER K 179 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP K 213 " --> pdb=" O PHE K 205 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR K 207 " --> pdb=" O LEU K 211 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU K 211 " --> pdb=" O TYR K 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 224 through 225 removed outlier: 3.591A pdb=" N VAL K 231 " --> pdb=" O THR K 238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 224 through 225 removed outlier: 6.519A pdb=" N GLU K 258 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE K 262 " --> pdb=" O GLU K 258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 276 through 283 removed outlier: 5.474A pdb=" N GLU K 277 " --> pdb=" O ARG K 292 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG K 292 " --> pdb=" O GLU K 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 352 through 356 removed outlier: 4.684A pdb=" N TRP K 352 " --> pdb=" O GLY K 363 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY K 363 " --> pdb=" O TRP K 352 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN K 402 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N GLU K 375 " --> pdb=" O ARG K 400 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N ARG K 400 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N PHE K 377 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 13.691A pdb=" N VAL K 398 " --> pdb=" O PHE K 377 " (cutoff:3.500A) removed outlier: 15.781A pdb=" N VAL K 379 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 16.488A pdb=" N VAL K 396 " --> pdb=" O VAL K 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 96 through 102 removed outlier: 3.632A pdb=" N GLY L 96 " --> pdb=" O THR L 449 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL L 445 " --> pdb=" O PHE L 100 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS L 102 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE L 443 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG L 420 " --> pdb=" O GLY L 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 115 through 124 removed outlier: 4.783A pdb=" N TRP L 115 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR L 138 " --> pdb=" O TRP L 115 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR L 117 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN L 136 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU L 119 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU L 134 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR L 157 " --> pdb=" O GLY L 135 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU L 158 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS L 172 " --> pdb=" O MET L 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 179 through 184 removed outlier: 3.652A pdb=" N SER L 179 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP L 197 " --> pdb=" O ASN L 200 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR L 207 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU L 211 " --> pdb=" O TYR L 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 231 through 233 removed outlier: 3.708A pdb=" N VAL L 231 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU L 258 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 276 through 283 removed outlier: 5.426A pdb=" N GLU L 277 " --> pdb=" O ARG L 292 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG L 292 " --> pdb=" O GLU L 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 353 through 356 removed outlier: 7.193A pdb=" N ASN L 402 " --> pdb=" O GLY L 373 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N GLU L 375 " --> pdb=" O ARG L 400 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N ARG L 400 " --> pdb=" O GLU L 375 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N PHE L 377 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 13.798A pdb=" N VAL L 398 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 15.842A pdb=" N VAL L 379 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 16.487A pdb=" N VAL L 396 " --> pdb=" O VAL L 379 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.543A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.593A pdb=" N LEU I 13 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3145 1.32 - 1.46: 5546 1.46 - 1.60: 10233 1.60 - 1.74: 1 1.74 - 1.88: 134 Bond restraints: 19059 Sorted by residual: bond pdb=" C VAL G 212 " pdb=" O VAL G 212 " ideal model delta sigma weight residual 1.237 1.293 -0.056 9.80e-03 1.04e+04 3.28e+01 bond pdb=" C THR K 225 " pdb=" O THR K 225 " ideal model delta sigma weight residual 1.236 1.289 -0.053 9.90e-03 1.02e+04 2.86e+01 bond pdb=" C THR K 195 " pdb=" O THR K 195 " ideal model delta sigma weight residual 1.234 1.298 -0.065 1.25e-02 6.40e+03 2.67e+01 bond pdb=" CE1 HIS K 274 " pdb=" NE2 HIS K 274 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.59e+01 bond pdb=" N GLU K 119 " pdb=" CA GLU K 119 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.40e-03 1.83e+04 2.27e+01 ... (remaining 19054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 18634 1.86 - 3.72: 6121 3.72 - 5.57: 981 5.57 - 7.43: 132 7.43 - 9.29: 9 Bond angle restraints: 25877 Sorted by residual: angle pdb=" CA ASP J 125 " pdb=" CB ASP J 125 " pdb=" CG ASP J 125 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.00e+00 1.00e+00 3.46e+01 angle pdb=" CA ASP L 125 " pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.21e+01 angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA PHE L 410 " pdb=" CB PHE L 410 " pdb=" CG PHE L 410 " ideal model delta sigma weight residual 113.80 119.21 -5.41 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA ASN C 105 " pdb=" C ASN C 105 " pdb=" O ASN C 105 " ideal model delta sigma weight residual 120.69 114.77 5.92 1.14e+00 7.69e-01 2.70e+01 ... (remaining 25872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9981 17.80 - 35.59: 490 35.59 - 53.38: 115 53.38 - 71.18: 26 71.18 - 88.97: 19 Dihedral angle restraints: 10631 sinusoidal: 4172 harmonic: 6459 Sorted by residual: dihedral pdb=" CA GLY K 297 " pdb=" C GLY K 297 " pdb=" N SER K 298 " pdb=" CA SER K 298 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CB CYS K 318 " pdb=" SG CYS K 318 " pdb=" SG CYS K 337 " pdb=" CB CYS K 337 " ideal model delta sinusoidal sigma weight residual 93.00 132.58 -39.58 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CB CYS L 318 " pdb=" SG CYS L 318 " pdb=" SG CYS L 337 " pdb=" CB CYS L 337 " ideal model delta sinusoidal sigma weight residual 93.00 131.98 -38.98 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 10628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2127 0.096 - 0.193: 869 0.193 - 0.289: 98 0.289 - 0.385: 1 0.385 - 0.482: 1 Chirality restraints: 3096 Sorted by residual: 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 5.68e+01 chirality pdb=" C1 FUC W 4 " pdb=" O6 NAG W 1 " pdb=" C2 FUC W 4 " pdb=" O5 FUC W 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.33e+01 chirality pdb=" C1 FUC t 4 " pdb=" O6 NAG t 1 " pdb=" C2 FUC t 4 " pdb=" O5 FUC t 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.27e+01 ... (remaining 3093 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.099 2.00e-02 2.50e+03 8.41e-02 8.84e+01 pdb=" C7 NAG T 2 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.123 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.087 2.00e-02 2.50e+03 7.50e-02 7.03e+01 pdb=" C7 NAG U 2 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.106 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.079 2.00e-02 2.50e+03 6.80e-02 5.78e+01 pdb=" C7 NAG S 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.001 2.00e-02 2.50e+03 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3914 2.83 - 3.35: 17131 3.35 - 3.87: 29899 3.87 - 4.38: 37700 4.38 - 4.90: 62546 Nonbonded interactions: 151190 Sorted by model distance: nonbonded pdb=" O HIS K 347 " pdb="CA CA K2000 " model vdw 2.313 2.510 nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.324 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G2000 " model vdw 2.326 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.339 2.510 nonbonded pdb=" O HIS L 347 " pdb="CA CA L 501 " model vdw 2.347 2.510 ... (remaining 151185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 82 through 501) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'q' } ncs_group { reference = (chain 'P' and resid 1 through 3) selection = (chain 'Q' and resid 1 through 3) selection = (chain 'R' and resid 1 through 3) selection = (chain 'V' and resid 1 through 3) selection = (chain 'W' and resid 1 through 3) selection = (chain 'X' and resid 1 through 3) selection = (chain 'r' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) } 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 'b' selection = chain 'c' selection = chain 'd' selection = chain 'v' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.170 19193 Z= 1.160 Angle : 1.848 16.390 26237 Z= 1.169 Chirality : 0.093 0.482 3096 Planarity : 0.011 0.084 3206 Dihedral : 12.385 88.973 6389 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 0.21 % Allowed : 2.83 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.86 (0.16), residues: 2252 helix: -1.10 (0.80), residues: 24 sheet: 0.24 (0.17), residues: 847 loop : -1.13 (0.14), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG K 156 TYR 0.077 0.014 TYR J 121 PHE 0.063 0.012 PHE K 205 TRP 0.086 0.014 TRP K 115 HIS 0.033 0.007 HIS K 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01631 / 1.15 (19059) covalent geometry : angle 1.78776 / 1.16 (25877) SS BOND : bond 0.06623 / 4.60 ( 42) SS BOND : angle 2.27860 / 1.58 ( 84) hydrogen bonds : bond 0.15792 / 10.44 ( 553) hydrogen bonds : angle 8.42271 / 5.98 ( 1497) link_ALPHA1-2 : bond 0.00367 / 0.17 ( 4) link_ALPHA1-2 : angle 4.77005 / 2.85 ( 12) link_ALPHA1-3 : bond 0.02231 / 1.27 ( 8) link_ALPHA1-3 : angle 4.11585 / 2.46 ( 24) link_ALPHA1-6 : bond 0.02145 / 1.33 ( 12) link_ALPHA1-6 : angle 3.16438 / 2.00 ( 36) link_BETA1-4 : bond 0.01686 / 1.06 ( 40) link_BETA1-4 : angle 4.38228 / 2.96 ( 120) link_BETA1-6 : bond 0.02248 / 1.00 ( 4) link_BETA1-6 : angle 4.71179 / 2.76 ( 12) link_NAG-ASN : bond 0.01934 / 1.20 ( 24) link_NAG-ASN : angle 6.29874 / 4.18 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7910 (tt0) cc_final: 0.7504 (tm-30) REVERT: F 42 GLN cc_start: 0.8434 (mt0) cc_final: 0.7773 (pp30) REVERT: F 93 ASN cc_start: 0.8666 (m-40) cc_final: 0.8242 (t0) REVERT: F 109 ARG cc_start: 0.7843 (ptm160) cc_final: 0.5768 (pmt170) REVERT: A 10 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7178 (mp0) REVERT: A 73 ASP cc_start: 0.7779 (t0) cc_final: 0.7500 (t0) REVERT: A 78 THR cc_start: 0.9051 (m) cc_final: 0.8746 (p) REVERT: D 1 GLU cc_start: 0.7832 (tt0) cc_final: 0.7398 (mm-30) REVERT: D 11 LEU cc_start: 0.8503 (tp) cc_final: 0.8173 (mp) REVERT: D 14 SER cc_start: 0.6749 (m) cc_final: 0.6204 (t) REVERT: D 50 ASP cc_start: 0.9250 (m-30) cc_final: 0.8645 (p0) REVERT: D 93 ASN cc_start: 0.8717 (m-40) cc_final: 0.8455 (t0) REVERT: K 101 SER cc_start: 0.9022 (t) cc_final: 0.8802 (m) REVERT: L 467 MET cc_start: 0.8848 (ptm) cc_final: 0.8643 (ptm) REVERT: C 12 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8655 (mppt) REVERT: I 1 GLU cc_start: 0.8120 (tt0) cc_final: 0.7861 (tp30) REVERT: I 11 LEU cc_start: 0.9166 (tp) cc_final: 0.8882 (tt) REVERT: I 13 LEU cc_start: 0.8531 (mt) cc_final: 0.8257 (tm) REVERT: I 106 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8156 (tm-30) outliers start: 4 outliers final: 1 residues processed: 285 average time/residue: 0.7189 time to fit residues: 227.6179 Evaluate side-chains 147 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 79 GLN F 89 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN D 6 GLN D 101 GLN K 147 ASN L 147 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068253 restraints weight = 36675.704| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.22 r_work: 0.2939 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19193 Z= 0.148 Angle : 0.764 9.563 26237 Z= 0.384 Chirality : 0.046 0.174 3096 Planarity : 0.004 0.044 3206 Dihedral : 5.702 28.880 2472 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 1.85 % Allowed : 9.98 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.57 (0.16), residues: 2252 helix: -0.55 (0.81), residues: 24 sheet: 0.18 (0.16), residues: 977 loop : -0.81 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.014 0.002 TYR G 121 PHE 0.016 0.002 PHE G 354 TRP 0.025 0.002 TRP J 178 HIS 0.004 0.001 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (19059) covalent geometry : angle 0.72788 / 0.38 (25877) SS BOND : bond 0.00379 / 0.22 ( 42) SS BOND : angle 1.14721 / 0.89 ( 84) hydrogen bonds : bond 0.04345 / 2.89 ( 553) hydrogen bonds : angle 6.83738 / 4.87 ( 1497) link_ALPHA1-2 : bond 0.00697 / 0.32 ( 4) link_ALPHA1-2 : angle 1.61442 / 0.86 ( 12) link_ALPHA1-3 : bond 0.00874 / 0.54 ( 8) link_ALPHA1-3 : angle 1.55479 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00801 / 0.47 ( 12) link_ALPHA1-6 : angle 1.45461 / 0.88 ( 36) link_BETA1-4 : bond 0.00649 / 0.43 ( 40) link_BETA1-4 : angle 2.28403 / 1.52 ( 120) link_BETA1-6 : bond 0.01705 / 0.77 ( 4) link_BETA1-6 : angle 1.54770 / 0.86 ( 12) link_NAG-ASN : bond 0.00491 / 0.30 ( 24) link_NAG-ASN : angle 3.08251 / 2.06 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 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: E 13 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8000 (mm-30) REVERT: E 80 TYR cc_start: 0.8435 (m-80) cc_final: 0.8217 (m-10) REVERT: E 81 MET cc_start: 0.7772 (tmm) cc_final: 0.7557 (tmm) REVERT: E 86 LEU cc_start: 0.7498 (mt) cc_final: 0.7156 (mp) REVERT: E 90 ASP cc_start: 0.7831 (m-30) cc_final: 0.7589 (m-30) REVERT: F 11 LEU cc_start: 0.8771 (tp) cc_final: 0.8525 (tp) REVERT: F 17 GLU cc_start: 0.8505 (mp0) cc_final: 0.7939 (mp0) REVERT: F 42 GLN cc_start: 0.8470 (mt0) cc_final: 0.7785 (pp30) REVERT: F 93 ASN cc_start: 0.8850 (m-40) cc_final: 0.8204 (t0) REVERT: F 109 ARG cc_start: 0.8548 (ptm160) cc_final: 0.6534 (pmt170) REVERT: J 362 MET cc_start: 0.8506 (ptp) cc_final: 0.8086 (ptt) REVERT: A 10 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7426 (mp0) REVERT: A 73 ASP cc_start: 0.7369 (t0) cc_final: 0.7046 (t0) REVERT: A 81 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7278 (ttp) REVERT: A 86 LEU cc_start: 0.7818 (mt) cc_final: 0.7521 (mp) REVERT: D 1 GLU cc_start: 0.7149 (tt0) cc_final: 0.6845 (mm-30) REVERT: D 11 LEU cc_start: 0.8591 (tp) cc_final: 0.8111 (mp) REVERT: D 50 ASP cc_start: 0.8935 (m-30) cc_final: 0.8220 (p0) REVERT: D 93 ASN cc_start: 0.8653 (m-40) cc_final: 0.8282 (t0) REVERT: K 101 SER cc_start: 0.9186 (t) cc_final: 0.8925 (t) REVERT: K 119 GLU cc_start: 0.8857 (mp0) cc_final: 0.8639 (mp0) REVERT: C 13 GLU cc_start: 0.8469 (mp0) cc_final: 0.7957 (pm20) REVERT: C 29 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6202 (m-10) REVERT: C 65 GLN cc_start: 0.7941 (tt0) cc_final: 0.7355 (mm110) REVERT: I 11 LEU cc_start: 0.8979 (tp) cc_final: 0.8684 (tt) REVERT: I 13 LEU cc_start: 0.8816 (mt) cc_final: 0.8370 (tm) REVERT: I 106 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7884 (tm-30) outliers start: 36 outliers final: 11 residues processed: 206 average time/residue: 0.7263 time to fit residues: 166.4219 Evaluate side-chains 154 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 29 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.064206 restraints weight = 38244.676| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.29 r_work: 0.2853 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.005 0.039 19193 Z= 0.230 Angle : 0.777 14.267 26237 Z= 0.388 Chirality : 0.048 0.270 3096 Planarity : 0.005 0.038 3206 Dihedral : 5.746 39.679 2470 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 2.21 % Allowed : 12.40 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.72 (0.16), residues: 2252 helix: -0.43 (0.94), residues: 24 sheet: 0.23 (0.17), residues: 947 loop : -1.04 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.023 0.002 TYR G 121 PHE 0.020 0.003 PHE G 354 TRP 0.021 0.002 TRP L 178 HIS 0.006 0.002 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (19059) covalent geometry : angle 0.73975 / 0.38 (25877) SS BOND : bond 0.00733 / 0.47 ( 42) SS BOND : angle 1.69563 / 1.23 ( 84) hydrogen bonds : bond 0.04463 / 2.96 ( 553) hydrogen bonds : angle 6.53905 / 4.65 ( 1497) link_ALPHA1-2 : bond 0.00475 / 0.20 ( 4) link_ALPHA1-2 : angle 2.20270 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00388 / 0.23 ( 8) link_ALPHA1-3 : angle 1.80889 / 1.10 ( 24) link_ALPHA1-6 : bond 0.00588 / 0.35 ( 12) link_ALPHA1-6 : angle 1.55433 / 0.95 ( 36) link_BETA1-4 : bond 0.00551 / 0.35 ( 40) link_BETA1-4 : angle 2.14231 / 1.41 ( 120) link_BETA1-6 : bond 0.01466 / 0.62 ( 4) link_BETA1-6 : angle 1.19796 / 0.67 ( 12) link_NAG-ASN : bond 0.00511 / 0.31 ( 24) link_NAG-ASN : angle 3.00176 / 2.01 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8185 (mtpp) REVERT: E 86 LEU cc_start: 0.7794 (mt) cc_final: 0.7418 (mp) REVERT: F 42 GLN cc_start: 0.8524 (mt0) cc_final: 0.7833 (pp30) REVERT: F 61 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7228 (mtm110) REVERT: F 82 ASP cc_start: 0.7669 (m-30) cc_final: 0.7439 (m-30) REVERT: F 93 ASN cc_start: 0.8961 (m-40) cc_final: 0.8363 (t0) REVERT: F 109 ARG cc_start: 0.8666 (ptm160) cc_final: 0.6860 (pmt170) REVERT: J 362 MET cc_start: 0.8622 (ptp) cc_final: 0.8233 (ptt) REVERT: A 10 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7578 (mp0) REVERT: A 57 THR cc_start: 0.7989 (m) cc_final: 0.7553 (t) REVERT: A 73 ASP cc_start: 0.7588 (t0) cc_final: 0.7365 (t0) REVERT: A 107 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8980 (m-30) REVERT: D 1 GLU cc_start: 0.7186 (tt0) cc_final: 0.6935 (mm-30) REVERT: D 11 LEU cc_start: 0.8708 (tp) cc_final: 0.8092 (mp) REVERT: D 50 ASP cc_start: 0.8931 (m-30) cc_final: 0.8258 (p0) REVERT: D 93 ASN cc_start: 0.8811 (m-40) cc_final: 0.8337 (t0) REVERT: K 119 GLU cc_start: 0.8917 (mp0) cc_final: 0.8542 (mp0) REVERT: C 10 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7375 (tm-30) REVERT: C 13 GLU cc_start: 0.8599 (mp0) cc_final: 0.8093 (pm20) REVERT: C 43 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8045 (mm110) REVERT: C 46 GLU cc_start: 0.7815 (tt0) cc_final: 0.7450 (tt0) REVERT: C 65 GLN cc_start: 0.8089 (tt0) cc_final: 0.7562 (mm-40) REVERT: C 73 ASP cc_start: 0.6423 (t0) cc_final: 0.6005 (t0) REVERT: C 120 GLN cc_start: 0.7761 (pm20) cc_final: 0.7245 (pm20) REVERT: I 4 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: I 11 LEU cc_start: 0.9056 (tp) cc_final: 0.8493 (tt) REVERT: I 13 LEU cc_start: 0.8825 (mt) cc_final: 0.8340 (tm) REVERT: I 35 TRP cc_start: 0.8027 (m100) cc_final: 0.6847 (m100) outliers start: 43 outliers final: 17 residues processed: 191 average time/residue: 0.6371 time to fit residues: 135.4753 Evaluate side-chains 157 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 27 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 205 optimal weight: 0.0370 chunk 18 optimal weight: 0.0970 chunk 194 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN K 441 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067002 restraints weight = 37761.143| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.26 r_work: 0.2918 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19193 Z= 0.118 Angle : 0.652 8.375 26237 Z= 0.324 Chirality : 0.044 0.191 3096 Planarity : 0.004 0.040 3206 Dihedral : 5.082 37.452 2470 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.84 % Favored : 96.98 % Rotamer: Outliers : 2.42 % Allowed : 12.76 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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 (0.17), residues: 2252 helix: -0.74 (1.00), residues: 24 sheet: 0.34 (0.17), residues: 969 loop : -0.78 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 24 TYR 0.010 0.001 TYR L 121 PHE 0.012 0.001 PHE K 410 TRP 0.019 0.001 TRP G 178 HIS 0.004 0.000 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (19059) covalent geometry : angle 0.62550 / 0.32 (25877) SS BOND : bond 0.00377 / 0.22 ( 42) SS BOND : angle 1.14714 / 0.83 ( 84) hydrogen bonds : bond 0.03416 / 2.26 ( 553) hydrogen bonds : angle 6.16151 / 4.40 ( 1497) link_ALPHA1-2 : bond 0.00794 / 0.36 ( 4) link_ALPHA1-2 : angle 1.80029 / 0.95 ( 12) link_ALPHA1-3 : bond 0.00762 / 0.49 ( 8) link_ALPHA1-3 : angle 1.40871 / 0.86 ( 24) link_ALPHA1-6 : bond 0.00676 / 0.41 ( 12) link_ALPHA1-6 : angle 1.39646 / 0.85 ( 36) link_BETA1-4 : bond 0.00519 / 0.34 ( 40) link_BETA1-4 : angle 1.68319 / 1.10 ( 120) link_BETA1-6 : bond 0.01315 / 0.56 ( 4) link_BETA1-6 : angle 1.24365 / 0.68 ( 12) link_NAG-ASN : bond 0.00334 / 0.20 ( 24) link_NAG-ASN : angle 2.32139 / 1.55 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7544 (p90) cc_final: 0.7247 (m-70) REVERT: E 23 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8130 (mtpp) REVERT: E 81 MET cc_start: 0.7873 (tmm) cc_final: 0.7403 (ppp) REVERT: E 86 LEU cc_start: 0.7858 (mt) cc_final: 0.7543 (mp) REVERT: F 42 GLN cc_start: 0.8468 (mt0) cc_final: 0.7842 (pp30) REVERT: F 61 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7149 (mtm110) REVERT: F 82 ASP cc_start: 0.7670 (m-30) cc_final: 0.7410 (m-30) REVERT: F 93 ASN cc_start: 0.8798 (m-40) cc_final: 0.8101 (t0) REVERT: F 109 ARG cc_start: 0.8523 (ptm160) cc_final: 0.6449 (ptp-170) REVERT: A 23 LYS cc_start: 0.8539 (tptm) cc_final: 0.8224 (tppp) REVERT: A 73 ASP cc_start: 0.7408 (t0) cc_final: 0.7083 (OUTLIER) REVERT: D 1 GLU cc_start: 0.7041 (tt0) cc_final: 0.6841 (mm-30) REVERT: D 3 VAL cc_start: 0.9240 (t) cc_final: 0.8918 (m) REVERT: D 11 LEU cc_start: 0.8697 (tp) cc_final: 0.8182 (mp) REVERT: D 93 ASN cc_start: 0.8679 (m-40) cc_final: 0.8135 (t0) REVERT: K 119 GLU cc_start: 0.8743 (mp0) cc_final: 0.8249 (mp0) REVERT: C 13 GLU cc_start: 0.8533 (mp0) cc_final: 0.8009 (pm20) REVERT: C 29 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: C 46 GLU cc_start: 0.7691 (tt0) cc_final: 0.7312 (tt0) REVERT: C 65 GLN cc_start: 0.7762 (tt0) cc_final: 0.7354 (mm-40) REVERT: C 102 ASP cc_start: 0.8884 (p0) cc_final: 0.8583 (p0) REVERT: I 4 MET cc_start: 0.7830 (mmm) cc_final: 0.7610 (mmm) REVERT: I 13 LEU cc_start: 0.8821 (mt) cc_final: 0.8327 (tm) REVERT: I 35 TRP cc_start: 0.7775 (m100) cc_final: 0.6480 (m100) outliers start: 47 outliers final: 20 residues processed: 198 average time/residue: 0.5928 time to fit residues: 131.0203 Evaluate side-chains 160 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 226 GLN G 294 ASN G 441 ASN E 62 GLN D 6 GLN K 226 GLN K 294 ASN L 226 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064749 restraints weight = 38056.300| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.11 r_work: 0.2919 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19193 Z= 0.267 Angle : 0.777 11.921 26237 Z= 0.387 Chirality : 0.049 0.260 3096 Planarity : 0.005 0.043 3206 Dihedral : 5.608 49.768 2470 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % Rotamer: Outliers : 3.09 % Allowed : 13.23 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.80 (0.17), residues: 2252 helix: -0.84 (0.97), residues: 24 sheet: 0.14 (0.17), residues: 954 loop : -1.05 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 87 TYR 0.021 0.002 TYR G 121 PHE 0.020 0.003 PHE J 422 TRP 0.019 0.002 TRP L 178 HIS 0.007 0.002 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 (19059) covalent geometry : angle 0.74326 / 0.38 (25877) SS BOND : bond 0.00600 / 0.34 ( 42) SS BOND : angle 1.51639 / 1.12 ( 84) hydrogen bonds : bond 0.04435 / 2.93 ( 553) hydrogen bonds : angle 6.39800 / 4.52 ( 1497) link_ALPHA1-2 : bond 0.00425 / 0.18 ( 4) link_ALPHA1-2 : angle 2.21798 / 1.20 ( 12) link_ALPHA1-3 : bond 0.00269 / 0.17 ( 8) link_ALPHA1-3 : angle 1.89959 / 1.15 ( 24) link_ALPHA1-6 : bond 0.00538 / 0.32 ( 12) link_ALPHA1-6 : angle 1.56789 / 0.95 ( 36) link_BETA1-4 : bond 0.00496 / 0.32 ( 40) link_BETA1-4 : angle 2.02543 / 1.34 ( 120) link_BETA1-6 : bond 0.01228 / 0.54 ( 4) link_BETA1-6 : angle 1.15946 / 0.65 ( 12) link_NAG-ASN : bond 0.00602 / 0.35 ( 24) link_NAG-ASN : angle 2.88118 / 1.93 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 146 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7633 (p90) cc_final: 0.7278 (m-70) REVERT: E 23 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8170 (mtpp) REVERT: E 86 LEU cc_start: 0.8034 (mt) cc_final: 0.7606 (mp) REVERT: F 24 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8106 (ttp-110) REVERT: F 61 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7136 (mtm110) REVERT: F 79 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7497 (mm110) REVERT: F 93 ASN cc_start: 0.8931 (m-40) cc_final: 0.8333 (t0) REVERT: F 109 ARG cc_start: 0.8574 (ptm160) cc_final: 0.6483 (ptp-170) REVERT: A 23 LYS cc_start: 0.8637 (tptm) cc_final: 0.8300 (tppp) REVERT: A 73 ASP cc_start: 0.7547 (t0) cc_final: 0.7345 (t0) REVERT: A 81 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7701 (ttt) REVERT: A 102 ASP cc_start: 0.9130 (p0) cc_final: 0.8908 (p0) REVERT: D 1 GLU cc_start: 0.7175 (tt0) cc_final: 0.6949 (mm-30) REVERT: D 3 VAL cc_start: 0.9291 (t) cc_final: 0.8960 (m) REVERT: D 11 LEU cc_start: 0.8782 (tp) cc_final: 0.8279 (mm) REVERT: D 37 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: D 93 ASN cc_start: 0.8810 (m-40) cc_final: 0.8290 (t0) REVERT: K 119 GLU cc_start: 0.8885 (mp0) cc_final: 0.8666 (mp0) REVERT: C 13 GLU cc_start: 0.8683 (mp0) cc_final: 0.8128 (pm20) REVERT: C 46 GLU cc_start: 0.8221 (tt0) cc_final: 0.7870 (tt0) REVERT: C 65 GLN cc_start: 0.8173 (tt0) cc_final: 0.7777 (mm-40) REVERT: C 102 ASP cc_start: 0.9155 (p0) cc_final: 0.8926 (p0) REVERT: I 4 MET cc_start: 0.8215 (mmm) cc_final: 0.7735 (mmm) REVERT: I 13 LEU cc_start: 0.8980 (mt) cc_final: 0.8488 (tm) REVERT: I 24 ARG cc_start: 0.6760 (tmm-80) cc_final: 0.6427 (tmm-80) REVERT: I 35 TRP cc_start: 0.8189 (m100) cc_final: 0.6950 (m100) REVERT: I 106 GLU cc_start: 0.8066 (pm20) cc_final: 0.7816 (pm20) outliers start: 60 outliers final: 28 residues processed: 191 average time/residue: 0.6133 time to fit residues: 131.2339 Evaluate side-chains 166 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain L residue 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 226 GLN G 294 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.094592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065629 restraints weight = 37643.480| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.14 r_work: 0.2938 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19193 Z= 0.185 Angle : 0.711 12.732 26237 Z= 0.354 Chirality : 0.046 0.195 3096 Planarity : 0.004 0.042 3206 Dihedral : 5.391 52.290 2470 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 2.88 % Allowed : 13.79 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.80 (0.17), residues: 2252 helix: -0.77 (1.02), residues: 24 sheet: 0.12 (0.17), residues: 967 loop : -1.05 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 87 TYR 0.016 0.001 TYR J 121 PHE 0.016 0.002 PHE G 410 TRP 0.020 0.002 TRP L 178 HIS 0.004 0.001 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (19059) covalent geometry : angle 0.68195 / 0.35 (25877) SS BOND : bond 0.00472 / 0.26 ( 42) SS BOND : angle 1.42015 / 1.03 ( 84) hydrogen bonds : bond 0.03928 / 2.60 ( 553) hydrogen bonds : angle 6.23430 / 4.41 ( 1497) link_ALPHA1-2 : bond 0.00555 / 0.24 ( 4) link_ALPHA1-2 : angle 2.09568 / 1.12 ( 12) link_ALPHA1-3 : bond 0.00465 / 0.30 ( 8) link_ALPHA1-3 : angle 1.65917 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00591 / 0.36 ( 12) link_ALPHA1-6 : angle 1.46472 / 0.88 ( 36) link_BETA1-4 : bond 0.00459 / 0.30 ( 40) link_BETA1-4 : angle 1.75585 / 1.16 ( 120) link_BETA1-6 : bond 0.01204 / 0.52 ( 4) link_BETA1-6 : angle 1.19891 / 0.66 ( 12) link_NAG-ASN : bond 0.00430 / 0.25 ( 24) link_NAG-ASN : angle 2.55014 / 1.71 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7757 (p90) cc_final: 0.7324 (m-70) REVERT: E 23 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8305 (mtpp) REVERT: E 86 LEU cc_start: 0.8104 (mt) cc_final: 0.7733 (mp) REVERT: F 24 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8101 (ttp-110) REVERT: F 61 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7297 (mtm110) REVERT: F 93 ASN cc_start: 0.8959 (m-40) cc_final: 0.8364 (t0) REVERT: F 109 ARG cc_start: 0.8587 (ptm160) cc_final: 0.6571 (ptp-170) REVERT: A 73 ASP cc_start: 0.7467 (t0) cc_final: 0.7196 (t0) REVERT: A 81 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7675 (ttt) REVERT: A 102 ASP cc_start: 0.9132 (p0) cc_final: 0.8877 (p0) REVERT: D 1 GLU cc_start: 0.7232 (tt0) cc_final: 0.6956 (mm-30) REVERT: D 3 VAL cc_start: 0.9362 (t) cc_final: 0.9047 (m) REVERT: D 4 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7745 (tpt) REVERT: D 11 LEU cc_start: 0.8754 (tp) cc_final: 0.8294 (mm) REVERT: D 24 ARG cc_start: 0.7705 (ppp80) cc_final: 0.7396 (ppp80) REVERT: D 93 ASN cc_start: 0.8853 (m-40) cc_final: 0.8188 (t0) REVERT: K 119 GLU cc_start: 0.8885 (mp0) cc_final: 0.8576 (mp0) REVERT: C 13 GLU cc_start: 0.8707 (mp0) cc_final: 0.8168 (pm20) REVERT: C 46 GLU cc_start: 0.8238 (tt0) cc_final: 0.7925 (tt0) REVERT: C 65 GLN cc_start: 0.8174 (tt0) cc_final: 0.7713 (mm-40) REVERT: C 73 ASP cc_start: 0.6785 (t0) cc_final: 0.6031 (t0) REVERT: C 102 ASP cc_start: 0.9147 (p0) cc_final: 0.8878 (p0) REVERT: I 4 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7967 (mmm) REVERT: I 13 LEU cc_start: 0.9058 (mt) cc_final: 0.8632 (tm) REVERT: I 24 ARG cc_start: 0.6795 (tmm-80) cc_final: 0.6494 (tmm-80) REVERT: I 35 TRP cc_start: 0.8172 (m100) cc_final: 0.6911 (m100) outliers start: 56 outliers final: 31 residues processed: 189 average time/residue: 0.6262 time to fit residues: 131.6200 Evaluate side-chains 169 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 211 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 0.4980 chunk 60 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 182 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 441 ASN E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067593 restraints weight = 37639.210| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.14 r_work: 0.2981 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19193 Z= 0.117 Angle : 0.664 11.818 26237 Z= 0.331 Chirality : 0.044 0.178 3096 Planarity : 0.004 0.051 3206 Dihedral : 5.011 48.360 2470 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 2.16 % Allowed : 14.87 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.59 (0.17), residues: 2252 helix: -0.83 (1.01), residues: 24 sheet: 0.26 (0.17), residues: 943 loop : -0.87 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 54 TYR 0.018 0.001 TYR F 49 PHE 0.014 0.001 PHE G 410 TRP 0.020 0.001 TRP G 178 HIS 0.003 0.000 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (19059) covalent geometry : angle 0.64102 / 0.33 (25877) SS BOND : bond 0.00380 / 0.22 ( 42) SS BOND : angle 1.16664 / 0.84 ( 84) hydrogen bonds : bond 0.03343 / 2.20 ( 553) hydrogen bonds : angle 6.01296 / 4.25 ( 1497) link_ALPHA1-2 : bond 0.00695 / 0.31 ( 4) link_ALPHA1-2 : angle 1.88895 / 1.00 ( 12) link_ALPHA1-3 : bond 0.00699 / 0.44 ( 8) link_ALPHA1-3 : angle 1.41033 / 0.86 ( 24) link_ALPHA1-6 : bond 0.00618 / 0.37 ( 12) link_ALPHA1-6 : angle 1.41693 / 0.86 ( 36) link_BETA1-4 : bond 0.00494 / 0.33 ( 40) link_BETA1-4 : angle 1.55959 / 1.02 ( 120) link_BETA1-6 : bond 0.01182 / 0.52 ( 4) link_BETA1-6 : angle 1.21065 / 0.66 ( 12) link_NAG-ASN : bond 0.00300 / 0.18 ( 24) link_NAG-ASN : angle 2.22398 / 1.48 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7374 (m-70) REVERT: E 23 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8291 (mtpp) REVERT: E 86 LEU cc_start: 0.8082 (mt) cc_final: 0.7711 (mp) REVERT: F 24 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8034 (ttp-110) REVERT: F 61 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7233 (mtm110) REVERT: F 93 ASN cc_start: 0.8930 (m-40) cc_final: 0.8348 (t0) REVERT: F 109 ARG cc_start: 0.8535 (ptm160) cc_final: 0.6591 (ptp-170) REVERT: J 128 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7891 (ptmt) REVERT: A 10 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 13 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 73 ASP cc_start: 0.7405 (t0) cc_final: 0.7126 (t0) REVERT: A 81 MET cc_start: 0.8032 (tmm) cc_final: 0.7173 (ttp) REVERT: A 102 ASP cc_start: 0.9020 (p0) cc_final: 0.8736 (p0) REVERT: D 1 GLU cc_start: 0.7252 (tt0) cc_final: 0.6959 (mm-30) REVERT: D 3 VAL cc_start: 0.9389 (t) cc_final: 0.9106 (m) REVERT: D 11 LEU cc_start: 0.8728 (tp) cc_final: 0.8279 (mm) REVERT: D 24 ARG cc_start: 0.7591 (ppp80) cc_final: 0.7318 (ppp80) REVERT: D 93 ASN cc_start: 0.8818 (m-40) cc_final: 0.8174 (t0) REVERT: D 109 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7437 (pmt170) REVERT: K 119 GLU cc_start: 0.8802 (mp0) cc_final: 0.8515 (mp0) REVERT: C 13 GLU cc_start: 0.8698 (mp0) cc_final: 0.8175 (pm20) REVERT: C 23 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8927 (mtpm) REVERT: C 29 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6309 (m-10) REVERT: C 46 GLU cc_start: 0.8163 (tt0) cc_final: 0.7881 (tt0) REVERT: C 65 GLN cc_start: 0.7936 (tt0) cc_final: 0.7452 (mm-40) REVERT: C 74 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7858 (pm20) REVERT: C 102 ASP cc_start: 0.9115 (p0) cc_final: 0.8830 (p0) REVERT: I 4 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: I 13 LEU cc_start: 0.9049 (mt) cc_final: 0.8611 (tm) REVERT: I 24 ARG cc_start: 0.6800 (tmm-80) cc_final: 0.6523 (tmm-80) REVERT: I 35 TRP cc_start: 0.8167 (m100) cc_final: 0.6916 (m100) REVERT: I 75 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8809 (tp) outliers start: 42 outliers final: 18 residues processed: 182 average time/residue: 0.6400 time to fit residues: 129.3929 Evaluate side-chains 161 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 14 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 92 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.092901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065177 restraints weight = 37645.035| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.99 r_work: 0.2926 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19193 Z= 0.249 Angle : 0.767 12.898 26237 Z= 0.382 Chirality : 0.048 0.197 3096 Planarity : 0.005 0.051 3206 Dihedral : 5.474 52.485 2470 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 2.21 % Allowed : 15.23 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.88 (0.17), residues: 2252 helix: -0.96 (0.99), residues: 24 sheet: 0.14 (0.17), residues: 903 loop : -1.12 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 87 TYR 0.020 0.002 TYR J 121 PHE 0.019 0.002 PHE J 422 TRP 0.015 0.002 TRP L 178 HIS 0.006 0.002 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (19059) covalent geometry : angle 0.73626 / 0.38 (25877) SS BOND : bond 0.00537 / 0.31 ( 42) SS BOND : angle 1.59357 / 1.09 ( 84) hydrogen bonds : bond 0.04279 / 2.82 ( 553) hydrogen bonds : angle 6.20545 / 4.39 ( 1497) link_ALPHA1-2 : bond 0.00431 / 0.19 ( 4) link_ALPHA1-2 : angle 2.12593 / 1.15 ( 12) link_ALPHA1-3 : bond 0.00286 / 0.18 ( 8) link_ALPHA1-3 : angle 1.81105 / 1.09 ( 24) link_ALPHA1-6 : bond 0.00510 / 0.31 ( 12) link_ALPHA1-6 : angle 1.53972 / 0.93 ( 36) link_BETA1-4 : bond 0.00463 / 0.30 ( 40) link_BETA1-4 : angle 1.89578 / 1.27 ( 120) link_BETA1-6 : bond 0.01188 / 0.51 ( 4) link_BETA1-6 : angle 1.13685 / 0.64 ( 12) link_NAG-ASN : bond 0.00562 / 0.33 ( 24) link_NAG-ASN : angle 2.73204 / 1.82 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7398 (m-70) REVERT: E 23 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8270 (mtpp) REVERT: E 86 LEU cc_start: 0.8145 (mt) cc_final: 0.7719 (mp) REVERT: F 24 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8188 (ttp-110) REVERT: F 61 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7347 (mtm110) REVERT: F 93 ASN cc_start: 0.8976 (m-40) cc_final: 0.8358 (t0) REVERT: F 109 ARG cc_start: 0.8558 (ptm160) cc_final: 0.6591 (ptp-170) REVERT: J 362 MET cc_start: 0.8505 (ptp) cc_final: 0.8217 (ptt) REVERT: A 10 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 23 LYS cc_start: 0.8609 (tptp) cc_final: 0.8322 (tppp) REVERT: A 73 ASP cc_start: 0.7436 (t0) cc_final: 0.7150 (t0) REVERT: A 81 MET cc_start: 0.8049 (tmm) cc_final: 0.7678 (ttt) REVERT: A 86 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7396 (pt) REVERT: A 102 ASP cc_start: 0.9029 (p0) cc_final: 0.8750 (p0) REVERT: D 1 GLU cc_start: 0.7308 (tt0) cc_final: 0.6891 (tm-30) REVERT: D 3 VAL cc_start: 0.9373 (t) cc_final: 0.9052 (m) REVERT: D 11 LEU cc_start: 0.8770 (tp) cc_final: 0.8294 (mm) REVERT: D 24 ARG cc_start: 0.7883 (ppp80) cc_final: 0.7338 (ppp80) REVERT: D 37 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: D 93 ASN cc_start: 0.8890 (m-40) cc_final: 0.8214 (t0) REVERT: D 109 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7403 (pmt170) REVERT: K 119 GLU cc_start: 0.8883 (mp0) cc_final: 0.8619 (mp0) REVERT: C 13 GLU cc_start: 0.8731 (mp0) cc_final: 0.8217 (pm20) REVERT: C 23 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8915 (mtpm) REVERT: C 46 GLU cc_start: 0.8252 (tt0) cc_final: 0.7980 (tt0) REVERT: C 65 GLN cc_start: 0.8250 (tt0) cc_final: 0.7753 (mm-40) REVERT: C 74 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7971 (pm20) REVERT: C 102 ASP cc_start: 0.9157 (p0) cc_final: 0.8896 (p0) REVERT: I 4 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (mmm) REVERT: I 13 LEU cc_start: 0.9073 (mt) cc_final: 0.8655 (tm) REVERT: I 24 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.6459 (tmm160) REVERT: I 35 TRP cc_start: 0.8176 (m100) cc_final: 0.6892 (m100) REVERT: I 75 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8819 (tp) outliers start: 43 outliers final: 19 residues processed: 169 average time/residue: 0.6514 time to fit residues: 121.7416 Evaluate side-chains 158 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 215 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 127 optimal weight: 0.0000 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.096123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067432 restraints weight = 37495.246| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.13 r_work: 0.2978 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19193 Z= 0.121 Angle : 0.670 11.822 26237 Z= 0.333 Chirality : 0.044 0.181 3096 Planarity : 0.004 0.046 3206 Dihedral : 4.981 48.253 2470 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 1.80 % Allowed : 15.59 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.67 (0.17), residues: 2252 helix: -0.80 (1.03), residues: 24 sheet: 0.26 (0.17), residues: 913 loop : -0.95 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 87 TYR 0.011 0.001 TYR K 121 PHE 0.014 0.001 PHE K 354 TRP 0.022 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (19059) covalent geometry : angle 0.64786 / 0.33 (25877) SS BOND : bond 0.00358 / 0.19 ( 42) SS BOND : angle 1.25125 / 0.84 ( 84) hydrogen bonds : bond 0.03354 / 2.20 ( 553) hydrogen bonds : angle 5.92208 / 4.20 ( 1497) link_ALPHA1-2 : bond 0.00697 / 0.31 ( 4) link_ALPHA1-2 : angle 1.87318 / 1.00 ( 12) link_ALPHA1-3 : bond 0.00635 / 0.40 ( 8) link_ALPHA1-3 : angle 1.40692 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00601 / 0.36 ( 12) link_ALPHA1-6 : angle 1.39890 / 0.85 ( 36) link_BETA1-4 : bond 0.00482 / 0.32 ( 40) link_BETA1-4 : angle 1.49780 / 0.99 ( 120) link_BETA1-6 : bond 0.01122 / 0.48 ( 4) link_BETA1-6 : angle 1.20621 / 0.66 ( 12) link_NAG-ASN : bond 0.00311 / 0.19 ( 24) link_NAG-ASN : angle 2.17786 / 1.45 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7448 (m-70) REVERT: E 23 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8350 (mtpp) REVERT: E 62 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7690 (tp-100) REVERT: E 81 MET cc_start: 0.7806 (tmm) cc_final: 0.7580 (ppp) REVERT: E 86 LEU cc_start: 0.8152 (mt) cc_final: 0.7767 (mp) REVERT: F 24 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8233 (ttp-110) REVERT: F 61 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7431 (mtm110) REVERT: F 93 ASN cc_start: 0.8923 (m-40) cc_final: 0.8317 (t0) REVERT: F 104 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8612 (tppp) REVERT: F 109 ARG cc_start: 0.8573 (ptm160) cc_final: 0.6616 (ptp-170) REVERT: A 10 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6989 (mm-30) REVERT: A 23 LYS cc_start: 0.8575 (tptp) cc_final: 0.8343 (tppp) REVERT: A 73 ASP cc_start: 0.7357 (t0) cc_final: 0.7086 (t0) REVERT: A 81 MET cc_start: 0.8048 (tmm) cc_final: 0.7737 (ttt) REVERT: A 86 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7466 (pt) REVERT: A 102 ASP cc_start: 0.9021 (p0) cc_final: 0.8743 (p0) REVERT: D 1 GLU cc_start: 0.7235 (tt0) cc_final: 0.6851 (tm-30) REVERT: D 3 VAL cc_start: 0.9378 (t) cc_final: 0.9086 (m) REVERT: D 11 LEU cc_start: 0.8722 (tp) cc_final: 0.8272 (mm) REVERT: D 81 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8173 (tp30) REVERT: D 93 ASN cc_start: 0.8845 (m-40) cc_final: 0.8165 (t0) REVERT: D 109 ARG cc_start: 0.7819 (ptm160) cc_final: 0.7437 (pmt170) REVERT: K 119 GLU cc_start: 0.8823 (mp0) cc_final: 0.8493 (mp0) REVERT: C 13 GLU cc_start: 0.8698 (mp0) cc_final: 0.8199 (pm20) REVERT: C 46 GLU cc_start: 0.8150 (tt0) cc_final: 0.7845 (tt0) REVERT: C 65 GLN cc_start: 0.7959 (tt0) cc_final: 0.7528 (mm-40) REVERT: C 74 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7857 (pm20) REVERT: C 87 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7292 (mtm110) REVERT: C 102 ASP cc_start: 0.9153 (p0) cc_final: 0.8870 (p0) REVERT: I 4 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8054 (mmm) REVERT: I 13 LEU cc_start: 0.9099 (mt) cc_final: 0.8689 (tm) REVERT: I 24 ARG cc_start: 0.6807 (tmm-80) cc_final: 0.6576 (tmm-80) REVERT: I 35 TRP cc_start: 0.8216 (m100) cc_final: 0.6956 (m100) REVERT: I 75 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8571 (tp) outliers start: 35 outliers final: 20 residues processed: 164 average time/residue: 0.6682 time to fit residues: 122.3728 Evaluate side-chains 158 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 117 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 188 optimal weight: 0.0170 chunk 174 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066370 restraints weight = 37697.554| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.12 r_work: 0.2953 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19193 Z= 0.173 Angle : 0.715 12.273 26237 Z= 0.356 Chirality : 0.045 0.183 3096 Planarity : 0.004 0.047 3206 Dihedral : 5.133 48.526 2470 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer: Outliers : 1.13 % Allowed : 16.31 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.72 (0.17), residues: 2252 helix: -0.81 (1.03), residues: 24 sheet: 0.25 (0.17), residues: 913 loop : -1.01 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 87 TYR 0.019 0.001 TYR F 49 PHE 0.016 0.002 PHE G 410 TRP 0.016 0.001 TRP G 178 HIS 0.004 0.001 HIS K 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (19059) covalent geometry : angle 0.68842 / 0.35 (25877) SS BOND : bond 0.00423 / 0.23 ( 42) SS BOND : angle 1.60437 / 1.06 ( 84) hydrogen bonds : bond 0.03699 / 2.43 ( 553) hydrogen bonds : angle 5.98115 / 4.23 ( 1497) link_ALPHA1-2 : bond 0.00571 / 0.25 ( 4) link_ALPHA1-2 : angle 1.94234 / 1.04 ( 12) link_ALPHA1-3 : bond 0.00443 / 0.28 ( 8) link_ALPHA1-3 : angle 1.54749 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00545 / 0.33 ( 12) link_ALPHA1-6 : angle 1.46648 / 0.89 ( 36) link_BETA1-4 : bond 0.00441 / 0.29 ( 40) link_BETA1-4 : angle 1.64497 / 1.09 ( 120) link_BETA1-6 : bond 0.01143 / 0.49 ( 4) link_BETA1-6 : angle 1.14856 / 0.63 ( 12) link_NAG-ASN : bond 0.00379 / 0.23 ( 24) link_NAG-ASN : angle 2.37400 / 1.58 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7428 (m-70) REVERT: E 23 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8351 (mtpp) REVERT: E 81 MET cc_start: 0.7808 (tmm) cc_final: 0.7564 (ppp) REVERT: E 86 LEU cc_start: 0.8147 (mt) cc_final: 0.7743 (mp) REVERT: F 24 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8218 (ttp-110) REVERT: F 61 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7450 (mtm110) REVERT: F 93 ASN cc_start: 0.8974 (m-40) cc_final: 0.8304 (t0) REVERT: F 104 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8619 (tppp) REVERT: F 109 ARG cc_start: 0.8458 (ptm160) cc_final: 0.6539 (ptp-170) REVERT: A 10 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 23 LYS cc_start: 0.8575 (tptp) cc_final: 0.8367 (tppp) REVERT: A 73 ASP cc_start: 0.7390 (t0) cc_final: 0.7110 (t0) REVERT: A 81 MET cc_start: 0.8028 (tmm) cc_final: 0.7732 (ttt) REVERT: A 102 ASP cc_start: 0.9015 (p0) cc_final: 0.8736 (p0) REVERT: D 1 GLU cc_start: 0.7252 (tt0) cc_final: 0.6813 (tm-30) REVERT: D 3 VAL cc_start: 0.9390 (t) cc_final: 0.9075 (m) REVERT: D 11 LEU cc_start: 0.8756 (tp) cc_final: 0.8291 (mm) REVERT: D 81 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8110 (tp30) REVERT: D 93 ASN cc_start: 0.8856 (m-40) cc_final: 0.8180 (t0) REVERT: D 109 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7437 (pmt170) REVERT: C 12 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8580 (mptm) REVERT: C 13 GLU cc_start: 0.8689 (mp0) cc_final: 0.8193 (pm20) REVERT: C 23 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8930 (mtpm) REVERT: C 46 GLU cc_start: 0.8188 (tt0) cc_final: 0.7891 (tt0) REVERT: C 65 GLN cc_start: 0.8120 (tt0) cc_final: 0.7746 (mm-40) REVERT: C 74 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7870 (pm20) REVERT: C 102 ASP cc_start: 0.9144 (p0) cc_final: 0.8862 (p0) REVERT: I 4 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: I 13 LEU cc_start: 0.9106 (mt) cc_final: 0.8680 (tm) REVERT: I 24 ARG cc_start: 0.6826 (tmm-80) cc_final: 0.6504 (tmm160) REVERT: I 35 TRP cc_start: 0.8219 (m100) cc_final: 0.6962 (m100) REVERT: I 75 ILE cc_start: 0.9145 (mt) cc_final: 0.8842 (tp) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.6835 time to fit residues: 111.3480 Evaluate side-chains 144 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 131 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.094948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066295 restraints weight = 37984.007| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.13 r_work: 0.2951 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19193 Z= 0.165 Angle : 0.707 12.424 26237 Z= 0.351 Chirality : 0.045 0.185 3096 Planarity : 0.004 0.047 3206 Dihedral : 5.150 48.824 2470 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 1.44 % Allowed : 15.90 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % 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: -0.76 (0.17), residues: 2252 helix: -0.82 (1.02), residues: 24 sheet: 0.26 (0.17), residues: 913 loop : -1.07 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 87 TYR 0.014 0.001 TYR J 121 PHE 0.016 0.002 PHE G 410 TRP 0.018 0.001 TRP L 178 HIS 0.004 0.001 HIS G 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (19059) covalent geometry : angle 0.68065 / 0.35 (25877) SS BOND : bond 0.00409 / 0.23 ( 42) SS BOND : angle 1.54002 / 1.02 ( 84) hydrogen bonds : bond 0.03699 / 2.43 ( 553) hydrogen bonds : angle 5.96575 / 4.22 ( 1497) link_ALPHA1-2 : bond 0.00541 / 0.24 ( 4) link_ALPHA1-2 : angle 1.99663 / 1.07 ( 12) link_ALPHA1-3 : bond 0.00450 / 0.28 ( 8) link_ALPHA1-3 : angle 1.55826 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00540 / 0.33 ( 12) link_ALPHA1-6 : angle 1.46601 / 0.88 ( 36) link_BETA1-4 : bond 0.00435 / 0.28 ( 40) link_BETA1-4 : angle 1.62394 / 1.08 ( 120) link_BETA1-6 : bond 0.01073 / 0.46 ( 4) link_BETA1-6 : angle 1.14328 / 0.63 ( 12) link_NAG-ASN : bond 0.00359 / 0.22 ( 24) link_NAG-ASN : angle 2.37175 / 1.58 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6523.29 seconds wall clock time: 112 minutes 6.19 seconds (6726.19 seconds total)