Starting phenix.real_space_refine on Sun Aug 24 09:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3m_29704/08_2025/8g3m_29704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3m_29704/08_2025/8g3m_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_29704/08_2025/8g3m_29704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3m_29704/08_2025/8g3m_29704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3m_29704/08_2025/8g3m_29704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3m_29704/08_2025/8g3m_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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 24 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 24 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 24 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 24 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 4.76, per 1000 atoms: 0.25 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: 2.24 Conformation dependent library (CDL) restraints added in 825.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.76 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: 3.79 Time building geometry restraints manager: 2.73 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 - 21.96: 11750 21.96 - 43.92: 473 43.92 - 65.88: 83 65.88 - 87.84: 99 87.84 - 109.81: 62 Dihedral angle restraints: 12467 sinusoidal: 6008 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 12464 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: 5.030 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.710 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 16.803 109.806 8225 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 aren 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 covalent geometry : bond 0.01631 (19059) covalent geometry : angle 1.78776 (25877) SS BOND : bond 0.06623 ( 42) SS BOND : angle 2.27860 ( 84) hydrogen bonds : bond 0.15792 ( 553) hydrogen bonds : angle 8.42271 ( 1497) link_ALPHA1-2 : bond 0.00367 ( 4) link_ALPHA1-2 : angle 4.77005 ( 12) link_ALPHA1-3 : bond 0.02231 ( 8) link_ALPHA1-3 : angle 4.11585 ( 24) link_ALPHA1-6 : bond 0.02145 ( 12) link_ALPHA1-6 : angle 3.16438 ( 36) link_BETA1-4 : bond 0.01686 ( 40) link_BETA1-4 : angle 4.38228 ( 120) link_BETA1-6 : bond 0.02248 ( 4) link_BETA1-6 : angle 4.71179 ( 12) link_NAG-ASN : bond 0.01934 ( 24) link_NAG-ASN : angle 6.29874 ( 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 : 0.741 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: 0.8747 (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: 0.7340 time to fit residues: 231.2504 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 : 0.748 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 J 147 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068290 restraints weight = 36694.827| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.22 r_work: 0.2939 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19193 Z= 0.149 Angle : 0.786 9.705 26237 Z= 0.388 Chirality : 0.048 0.185 3096 Planarity : 0.004 0.043 3206 Dihedral : 13.128 80.434 4308 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 10.04 % Favored : 88.21 % 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 aren not related in a simple way. whole: -0.54 (0.16), residues: 2252 helix: -0.73 (0.78), residues: 24 sheet: 0.22 (0.16), residues: 973 loop : -0.80 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.013 0.002 TYR G 281 PHE 0.016 0.002 PHE G 354 TRP 0.025 0.002 TRP L 178 HIS 0.004 0.001 HIS L 347 Details of bonding type rmsd covalent geometry : bond 0.00308 (19059) covalent geometry : angle 0.74276 (25877) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.17668 ( 84) hydrogen bonds : bond 0.04213 ( 553) hydrogen bonds : angle 6.79143 ( 1497) link_ALPHA1-2 : bond 0.00813 ( 4) link_ALPHA1-2 : angle 1.81594 ( 12) link_ALPHA1-3 : bond 0.01177 ( 8) link_ALPHA1-3 : angle 2.04417 ( 24) link_ALPHA1-6 : bond 0.00872 ( 12) link_ALPHA1-6 : angle 1.59797 ( 36) link_BETA1-4 : bond 0.00697 ( 40) link_BETA1-4 : angle 2.74345 ( 120) link_BETA1-6 : bond 0.01920 ( 4) link_BETA1-6 : angle 1.62374 ( 12) link_NAG-ASN : bond 0.00530 ( 24) link_NAG-ASN : angle 3.03393 ( 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 216 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.826 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: 0.8235 (mm-30) cc_final: 0.8019 (mm-30) REVERT: E 81 MET cc_start: 0.7792 (tmm) cc_final: 0.7321 (ppp) REVERT: E 86 LEU cc_start: 0.7537 (mt) cc_final: 0.7208 (mp) REVERT: E 90 ASP cc_start: 0.7856 (m-30) cc_final: 0.7601 (m-30) REVERT: F 11 LEU cc_start: 0.8785 (tp) cc_final: 0.8576 (tp) REVERT: F 42 GLN cc_start: 0.8463 (mt0) cc_final: 0.7786 (pp30) REVERT: F 93 ASN cc_start: 0.8850 (m-40) cc_final: 0.8271 (t0) REVERT: F 109 ARG cc_start: 0.8581 (ptm160) cc_final: 0.6538 (pmt170) REVERT: A 10 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7398 (mp0) REVERT: A 73 ASP cc_start: 0.7365 (t0) cc_final: 0.7007 (OUTLIER) REVERT: A 80 TYR cc_start: 0.8485 (m-80) cc_final: 0.8275 (m-10) REVERT: A 86 LEU cc_start: 0.7849 (mt) cc_final: 0.7555 (mp) REVERT: D 1 GLU cc_start: 0.7156 (tt0) cc_final: 0.6854 (mm-30) REVERT: D 11 LEU cc_start: 0.8604 (tp) cc_final: 0.8111 (mp) REVERT: D 50 ASP cc_start: 0.8933 (m-30) cc_final: 0.8219 (p0) REVERT: D 93 ASN cc_start: 0.8650 (m-40) cc_final: 0.8298 (t0) REVERT: K 101 SER cc_start: 0.9190 (t) cc_final: 0.8932 (t) REVERT: K 119 GLU cc_start: 0.8838 (mp0) cc_final: 0.8633 (mp0) REVERT: C 13 GLU cc_start: 0.8472 (mp0) cc_final: 0.7943 (pm20) REVERT: C 29 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6245 (m-10) REVERT: C 46 GLU cc_start: 0.7634 (tp30) cc_final: 0.7389 (tt0) REVERT: C 65 GLN cc_start: 0.7920 (tt0) cc_final: 0.7335 (mm110) REVERT: I 11 LEU cc_start: 0.8985 (tp) cc_final: 0.8681 (tt) REVERT: I 13 LEU cc_start: 0.8816 (mt) cc_final: 0.8369 (tm) REVERT: I 106 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7832 (tm-30) outliers start: 34 outliers final: 12 residues processed: 205 average time/residue: 0.7280 time to fit residues: 165.2165 Evaluate side-chains 157 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 128 SER 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 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: 0.8980 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 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: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064904 restraints weight = 37826.500| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.16 r_work: 0.2873 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19193 Z= 0.244 Angle : 0.818 14.304 26237 Z= 0.402 Chirality : 0.051 0.264 3096 Planarity : 0.005 0.038 3206 Dihedral : 10.436 68.023 4306 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 12.66 % Favored : 85.13 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2252 helix: -0.59 (0.93), residues: 24 sheet: 0.19 (0.16), residues: 950 loop : -1.05 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 18 TYR 0.024 0.002 TYR G 121 PHE 0.020 0.003 PHE G 354 TRP 0.022 0.002 TRP L 178 HIS 0.007 0.002 HIS L 184 Details of bonding type rmsd covalent geometry : bond 0.00571 (19059) covalent geometry : angle 0.77148 (25877) SS BOND : bond 0.00659 ( 42) SS BOND : angle 1.97918 ( 84) hydrogen bonds : bond 0.04579 ( 553) hydrogen bonds : angle 6.56887 ( 1497) link_ALPHA1-2 : bond 0.00424 ( 4) link_ALPHA1-2 : angle 2.37770 ( 12) link_ALPHA1-3 : bond 0.00658 ( 8) link_ALPHA1-3 : angle 2.15694 ( 24) link_ALPHA1-6 : bond 0.00726 ( 12) link_ALPHA1-6 : angle 1.50453 ( 36) link_BETA1-4 : bond 0.00627 ( 40) link_BETA1-4 : angle 2.70474 ( 120) link_BETA1-6 : bond 0.01366 ( 4) link_BETA1-6 : angle 1.27787 ( 12) link_NAG-ASN : bond 0.00530 ( 24) link_NAG-ASN : angle 3.05839 ( 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 : 0.881 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: 0.8578 (mtpp) cc_final: 0.8147 (mtpp) REVERT: E 86 LEU cc_start: 0.7826 (mt) cc_final: 0.7447 (mp) REVERT: F 42 GLN cc_start: 0.8493 (mt0) cc_final: 0.7797 (pp30) REVERT: F 82 ASP cc_start: 0.7553 (m-30) cc_final: 0.7308 (m-30) REVERT: F 93 ASN cc_start: 0.8942 (m-40) cc_final: 0.8331 (t0) REVERT: F 109 ARG cc_start: 0.8719 (ptm160) cc_final: 0.6859 (pmt170) REVERT: J 362 MET cc_start: 0.8615 (ptp) cc_final: 0.8258 (ptt) REVERT: A 10 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7590 (mp0) REVERT: A 57 THR cc_start: 0.8080 (m) cc_final: 0.7649 (t) REVERT: A 73 ASP cc_start: 0.7612 (t0) cc_final: 0.7381 (t0) REVERT: A 107 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: D 1 GLU cc_start: 0.7265 (tt0) cc_final: 0.7002 (mm-30) REVERT: D 11 LEU cc_start: 0.8719 (tp) cc_final: 0.8109 (mp) REVERT: D 50 ASP cc_start: 0.8943 (m-30) cc_final: 0.8259 (p0) REVERT: D 93 ASN cc_start: 0.8839 (m-40) cc_final: 0.8348 (t0) REVERT: C 10 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7400 (tm-30) REVERT: C 13 GLU cc_start: 0.8572 (mp0) cc_final: 0.8061 (pm20) REVERT: C 43 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8021 (mm110) REVERT: C 46 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: C 65 GLN cc_start: 0.8202 (tt0) cc_final: 0.7761 (mm-40) REVERT: C 73 ASP cc_start: 0.6442 (t0) cc_final: 0.6025 (t0) REVERT: I 4 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: I 11 LEU cc_start: 0.9048 (tp) cc_final: 0.8466 (tt) REVERT: I 13 LEU cc_start: 0.8829 (mt) cc_final: 0.8338 (tm) REVERT: I 24 ARG cc_start: 0.6555 (tmm-80) cc_final: 0.6251 (tmm-80) REVERT: I 35 TRP cc_start: 0.8048 (m100) cc_final: 0.6796 (m100) outliers start: 43 outliers final: 17 residues processed: 190 average time/residue: 0.7192 time to fit residues: 151.6724 Evaluate side-chains 157 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 C residue 46 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 27 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 205 optimal weight: 0.0010 chunk 18 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 199 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3625 r_free = 0.3625 target = 0.096022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067607 restraints weight = 37563.013| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.15 r_work: 0.2935 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19193 Z= 0.120 Angle : 0.687 8.945 26237 Z= 0.336 Chirality : 0.046 0.193 3096 Planarity : 0.004 0.040 3206 Dihedral : 7.869 57.095 4306 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 2.62 % Allowed : 12.51 % Favored : 84.87 % 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 aren not related in a simple way. whole: -0.53 (0.17), residues: 2252 helix: -0.70 (1.02), residues: 24 sheet: 0.28 (0.17), residues: 969 loop : -0.85 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 63 TYR 0.012 0.001 TYR G 121 PHE 0.012 0.002 PHE K 410 TRP 0.019 0.001 TRP L 178 HIS 0.004 0.001 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00260 (19059) covalent geometry : angle 0.65265 (25877) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.21601 ( 84) hydrogen bonds : bond 0.03491 ( 553) hydrogen bonds : angle 6.19272 ( 1497) link_ALPHA1-2 : bond 0.00664 ( 4) link_ALPHA1-2 : angle 2.14974 ( 12) link_ALPHA1-3 : bond 0.01045 ( 8) link_ALPHA1-3 : angle 1.63146 ( 24) link_ALPHA1-6 : bond 0.00837 ( 12) link_ALPHA1-6 : angle 1.42426 ( 36) link_BETA1-4 : bond 0.00577 ( 40) link_BETA1-4 : angle 2.23921 ( 120) link_BETA1-6 : bond 0.01163 ( 4) link_BETA1-6 : angle 1.28304 ( 12) link_NAG-ASN : bond 0.00341 ( 24) link_NAG-ASN : angle 2.38078 ( 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 215 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.754 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: 0.7605 (p90) cc_final: 0.7345 (m-70) REVERT: E 23 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8084 (mtpp) REVERT: E 81 MET cc_start: 0.7936 (tmm) cc_final: 0.7465 (ppp) REVERT: E 86 LEU cc_start: 0.7833 (mt) cc_final: 0.7485 (mp) REVERT: F 42 GLN cc_start: 0.8519 (mt0) cc_final: 0.7845 (pp30) REVERT: F 61 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7345 (mtm110) REVERT: F 82 ASP cc_start: 0.7564 (m-30) cc_final: 0.7287 (m-30) REVERT: F 93 ASN cc_start: 0.8934 (m-40) cc_final: 0.8289 (t0) REVERT: F 109 ARG cc_start: 0.8567 (ptm160) cc_final: 0.6464 (ptp-170) REVERT: A 10 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7588 (mp0) REVERT: A 73 ASP cc_start: 0.7355 (t0) cc_final: 0.7140 (t0) REVERT: A 81 MET cc_start: 0.7549 (ttp) cc_final: 0.6987 (ttp) REVERT: A 107 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8904 (m-30) REVERT: D 1 GLU cc_start: 0.7218 (tt0) cc_final: 0.6924 (mm-30) REVERT: D 3 VAL cc_start: 0.9256 (t) cc_final: 0.8925 (m) REVERT: D 4 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7781 (tpt) REVERT: D 11 LEU cc_start: 0.8687 (tp) cc_final: 0.8218 (mp) REVERT: D 93 ASN cc_start: 0.8818 (m-40) cc_final: 0.8265 (t0) REVERT: K 119 GLU cc_start: 0.8857 (mp0) cc_final: 0.8384 (mp0) REVERT: C 13 GLU cc_start: 0.8586 (mp0) cc_final: 0.8025 (pm20) REVERT: C 29 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6646 (m-10) REVERT: C 46 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: C 65 GLN cc_start: 0.7829 (tt0) cc_final: 0.7377 (mm-40) REVERT: C 74 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7952 (pm20) REVERT: C 102 ASP cc_start: 0.8996 (p0) cc_final: 0.8686 (p0) REVERT: I 13 LEU cc_start: 0.8810 (mt) cc_final: 0.8302 (tm) REVERT: I 24 ARG cc_start: 0.6593 (tmm-80) cc_final: 0.6210 (tmm-80) REVERT: I 35 TRP cc_start: 0.7968 (m100) cc_final: 0.6718 (m100) outliers start: 51 outliers final: 23 residues processed: 199 average time/residue: 0.6840 time to fit residues: 151.4984 Evaluate side-chains 167 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 10 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 215 VAL 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 88 SER Chi-restraints excluded: chain A residue 107 ASP 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 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 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 46 GLU 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: 0.7980 chunk 111 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN 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 = 0.3623 r_free = 0.3623 target = 0.095811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066707 restraints weight = 37398.241| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.22 r_work: 0.2930 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19193 Z= 0.138 Angle : 0.686 11.922 26237 Z= 0.337 Chirality : 0.046 0.194 3096 Planarity : 0.004 0.042 3206 Dihedral : 7.214 53.677 4306 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 2.88 % Allowed : 13.28 % Favored : 83.84 % 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 aren not related in a simple way. whole: -0.42 (0.17), residues: 2252 helix: -0.52 (1.03), residues: 24 sheet: 0.36 (0.17), residues: 961 loop : -0.77 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 87 TYR 0.015 0.001 TYR G 121 PHE 0.014 0.002 PHE J 354 TRP 0.017 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00319 (19059) covalent geometry : angle 0.65425 (25877) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.29662 ( 84) hydrogen bonds : bond 0.03521 ( 553) hydrogen bonds : angle 6.13671 ( 1497) link_ALPHA1-2 : bond 0.00644 ( 4) link_ALPHA1-2 : angle 2.14292 ( 12) link_ALPHA1-3 : bond 0.00934 ( 8) link_ALPHA1-3 : angle 1.72766 ( 24) link_ALPHA1-6 : bond 0.00760 ( 12) link_ALPHA1-6 : angle 1.39046 ( 36) link_BETA1-4 : bond 0.00538 ( 40) link_BETA1-4 : angle 2.05026 ( 120) link_BETA1-6 : bond 0.01227 ( 4) link_BETA1-6 : angle 1.24774 ( 12) link_NAG-ASN : bond 0.00312 ( 24) link_NAG-ASN : angle 2.40513 ( 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 207 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7540 (p90) cc_final: 0.7296 (m-70) REVERT: E 23 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8135 (mtpp) REVERT: E 86 LEU cc_start: 0.7873 (mt) cc_final: 0.7487 (mp) REVERT: F 93 ASN cc_start: 0.8950 (m-40) cc_final: 0.8272 (t0) REVERT: F 109 ARG cc_start: 0.8531 (ptm160) cc_final: 0.6433 (ptp-170) REVERT: A 73 ASP cc_start: 0.7239 (t0) cc_final: 0.6956 (t0) REVERT: A 76 THR cc_start: 0.9157 (p) cc_final: 0.8952 (t) REVERT: A 81 MET cc_start: 0.7555 (ttp) cc_final: 0.7055 (ttp) REVERT: A 102 ASP cc_start: 0.9069 (p0) cc_final: 0.8832 (p0) REVERT: A 107 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8952 (m-30) REVERT: D 1 GLU cc_start: 0.7228 (tt0) cc_final: 0.6900 (mm-30) REVERT: D 3 VAL cc_start: 0.9287 (t) cc_final: 0.8958 (m) REVERT: D 11 LEU cc_start: 0.8688 (tp) cc_final: 0.8163 (mp) REVERT: D 93 ASN cc_start: 0.8831 (m-40) cc_final: 0.8266 (t0) REVERT: K 119 GLU cc_start: 0.8858 (mp0) cc_final: 0.8455 (mp0) REVERT: C 13 GLU cc_start: 0.8623 (mp0) cc_final: 0.8060 (pm20) REVERT: C 46 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: C 65 GLN cc_start: 0.7842 (tt0) cc_final: 0.7306 (mm-40) REVERT: C 74 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7970 (pm20) REVERT: C 102 ASP cc_start: 0.8997 (p0) cc_final: 0.8702 (p0) REVERT: I 4 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: I 13 LEU cc_start: 0.8919 (mt) cc_final: 0.8431 (tm) REVERT: I 24 ARG cc_start: 0.6669 (tmm-80) cc_final: 0.6289 (tmm-80) REVERT: I 35 TRP cc_start: 0.7985 (m100) cc_final: 0.6713 (m100) REVERT: I 75 ILE cc_start: 0.9126 (mt) cc_final: 0.8702 (tp) outliers start: 56 outliers final: 26 residues processed: 190 average time/residue: 0.6757 time to fit residues: 143.1493 Evaluate side-chains 168 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 176 ILE Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 318 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 ASP 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 K residue 124 CYS Chi-restraints excluded: chain K residue 229 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 L residue 376 THR Chi-restraints excluded: chain L residue 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain I residue 4 MET 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: 0.8980 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 171 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN K 226 GLN L 226 GLN ** 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 = 0.3585 r_free = 0.3585 target = 0.093498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064397 restraints weight = 37828.214| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.23 r_work: 0.2878 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19193 Z= 0.232 Angle : 0.752 13.100 26237 Z= 0.373 Chirality : 0.048 0.208 3096 Planarity : 0.004 0.043 3206 Dihedral : 7.521 56.761 4306 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Rotamer: Outliers : 2.99 % Allowed : 13.59 % Favored : 83.43 % 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 aren not related in a simple way. whole: -0.74 (0.17), residues: 2252 helix: -0.85 (0.99), residues: 24 sheet: 0.21 (0.17), residues: 951 loop : -1.03 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 87 TYR 0.021 0.002 TYR G 121 PHE 0.018 0.002 PHE J 422 TRP 0.018 0.002 TRP L 178 HIS 0.006 0.002 HIS G 144 Details of bonding type rmsd covalent geometry : bond 0.00550 (19059) covalent geometry : angle 0.71762 (25877) SS BOND : bond 0.00582 ( 42) SS BOND : angle 1.41782 ( 84) hydrogen bonds : bond 0.04198 ( 553) hydrogen bonds : angle 6.26212 ( 1497) link_ALPHA1-2 : bond 0.00430 ( 4) link_ALPHA1-2 : angle 2.34597 ( 12) link_ALPHA1-3 : bond 0.00655 ( 8) link_ALPHA1-3 : angle 2.21168 ( 24) link_ALPHA1-6 : bond 0.00677 ( 12) link_ALPHA1-6 : angle 1.43915 ( 36) link_BETA1-4 : bond 0.00518 ( 40) link_BETA1-4 : angle 2.06832 ( 120) link_BETA1-6 : bond 0.01195 ( 4) link_BETA1-6 : angle 1.21959 ( 12) link_NAG-ASN : bond 0.00524 ( 24) link_NAG-ASN : angle 2.74991 ( 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 211 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7633 (p90) cc_final: 0.7267 (m-70) REVERT: E 23 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8197 (mtpp) REVERT: E 46 GLU cc_start: 0.8323 (tt0) cc_final: 0.8065 (tt0) REVERT: E 86 LEU cc_start: 0.7923 (mt) cc_final: 0.7509 (mp) REVERT: F 24 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.8071 (mmm-85) REVERT: F 61 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7339 (mtm110) REVERT: F 82 ASP cc_start: 0.7681 (m-30) cc_final: 0.7434 (m-30) REVERT: F 93 ASN cc_start: 0.9014 (m-40) cc_final: 0.8303 (t0) REVERT: F 109 ARG cc_start: 0.8511 (ptm160) cc_final: 0.6444 (ptp-170) REVERT: A 73 ASP cc_start: 0.7303 (t0) cc_final: 0.7009 (t0) REVERT: A 102 ASP cc_start: 0.9097 (p0) cc_final: 0.8835 (p0) REVERT: A 107 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8991 (m-30) REVERT: D 1 GLU cc_start: 0.7291 (tt0) cc_final: 0.6947 (mm-30) REVERT: D 3 VAL cc_start: 0.9321 (t) cc_final: 0.8987 (m) REVERT: D 11 LEU cc_start: 0.8704 (tp) cc_final: 0.8160 (mp) REVERT: D 37 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: D 93 ASN cc_start: 0.8908 (m-40) cc_final: 0.8148 (t0) REVERT: K 119 GLU cc_start: 0.8898 (mp0) cc_final: 0.8559 (mp0) REVERT: K 150 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8133 (mtm180) REVERT: C 13 GLU cc_start: 0.8686 (mp0) cc_final: 0.8159 (pm20) REVERT: C 29 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: C 46 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: C 65 GLN cc_start: 0.8016 (tt0) cc_final: 0.7510 (mm-40) REVERT: C 74 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8043 (pm20) REVERT: C 102 ASP cc_start: 0.9058 (p0) cc_final: 0.8818 (p0) REVERT: I 4 MET cc_start: 0.8096 (mmm) cc_final: 0.7226 (mmm) REVERT: I 13 LEU cc_start: 0.9025 (mt) cc_final: 0.8583 (tm) REVERT: I 24 ARG cc_start: 0.6721 (tmm-80) cc_final: 0.6371 (tmm-80) REVERT: I 35 TRP cc_start: 0.8019 (m100) cc_final: 0.6756 (m100) REVERT: I 88 CYS cc_start: 0.7332 (p) cc_final: 0.6538 (p) outliers start: 58 outliers final: 31 residues processed: 196 average time/residue: 0.7342 time to fit residues: 159.4785 Evaluate side-chains 172 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP 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 128 LYS 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 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 107 ASP Chi-restraints excluded: chain D residue 14 SER 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 148 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 L residue 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 46 GLU 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: 4.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066730 restraints weight = 37663.355| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.24 r_work: 0.2929 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19193 Z= 0.125 Angle : 0.675 11.791 26237 Z= 0.334 Chirality : 0.045 0.186 3096 Planarity : 0.004 0.045 3206 Dihedral : 6.851 49.688 4306 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 2.57 % Allowed : 14.20 % Favored : 83.22 % 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 aren not related in a simple way. whole: -0.58 (0.17), residues: 2252 helix: -0.76 (1.03), residues: 24 sheet: 0.26 (0.16), residues: 967 loop : -0.89 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 54 TYR 0.011 0.001 TYR G 121 PHE 0.014 0.001 PHE G 410 TRP 0.019 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00283 (19059) covalent geometry : angle 0.64942 (25877) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.17435 ( 84) hydrogen bonds : bond 0.03387 ( 553) hydrogen bonds : angle 6.02147 ( 1497) link_ALPHA1-2 : bond 0.00634 ( 4) link_ALPHA1-2 : angle 2.25779 ( 12) link_ALPHA1-3 : bond 0.01042 ( 8) link_ALPHA1-3 : angle 1.67625 ( 24) link_ALPHA1-6 : bond 0.00756 ( 12) link_ALPHA1-6 : angle 1.31152 ( 36) link_BETA1-4 : bond 0.00535 ( 40) link_BETA1-4 : angle 1.69227 ( 120) link_BETA1-6 : bond 0.01113 ( 4) link_BETA1-6 : angle 1.28870 ( 12) link_NAG-ASN : bond 0.00313 ( 24) link_NAG-ASN : angle 2.26134 ( 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 196 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.727 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: 0.7726 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: E 23 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8283 (mtpp) REVERT: E 86 LEU cc_start: 0.7990 (mt) cc_final: 0.7620 (mp) REVERT: F 24 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8160 (ttp-110) REVERT: F 61 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7287 (mtm110) REVERT: F 82 ASP cc_start: 0.7623 (m-30) cc_final: 0.7375 (m-30) REVERT: F 93 ASN cc_start: 0.8837 (m-40) cc_final: 0.8126 (t0) REVERT: F 109 ARG cc_start: 0.8469 (ptm160) cc_final: 0.6546 (ptp-170) REVERT: A 10 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 13 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 73 ASP cc_start: 0.7255 (t0) cc_final: 0.7005 (t0) REVERT: A 102 ASP cc_start: 0.8888 (p0) cc_final: 0.8604 (p0) REVERT: D 1 GLU cc_start: 0.7166 (tt0) cc_final: 0.6888 (mm-30) REVERT: D 3 VAL cc_start: 0.9377 (t) cc_final: 0.9099 (m) REVERT: D 11 LEU cc_start: 0.8681 (tp) cc_final: 0.8214 (mm) REVERT: D 37 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: D 93 ASN cc_start: 0.8751 (m-40) cc_final: 0.7994 (t0) REVERT: K 119 GLU cc_start: 0.8778 (mp0) cc_final: 0.8324 (mp0) REVERT: C 13 GLU cc_start: 0.8634 (mp0) cc_final: 0.8107 (pm20) REVERT: C 65 GLN cc_start: 0.7850 (tt0) cc_final: 0.7362 (mm-40) REVERT: C 74 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7934 (pm20) REVERT: C 102 ASP cc_start: 0.8964 (p0) cc_final: 0.8657 (p0) REVERT: I 4 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7324 (mmm) REVERT: I 13 LEU cc_start: 0.9039 (mt) cc_final: 0.8599 (tm) REVERT: I 24 ARG cc_start: 0.6759 (tmm-80) cc_final: 0.6461 (tmm-80) REVERT: I 35 TRP cc_start: 0.7885 (m100) cc_final: 0.6613 (m100) REVERT: I 75 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8796 (tp) REVERT: I 88 CYS cc_start: 0.6687 (p) cc_final: 0.6136 (p) outliers start: 50 outliers final: 23 residues processed: 185 average time/residue: 0.6948 time to fit residues: 143.0686 Evaluate side-chains 163 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 110 THR Chi-restraints excluded: chain J residue 128 LYS 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 D residue 14 SER 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 148 THR 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 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain I residue 2 ILE 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: 2.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN G 441 ASN J 226 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 HIS D 32 ASN D 92 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064057 restraints weight = 38118.219| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.23 r_work: 0.2870 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19193 Z= 0.250 Angle : 0.766 12.834 26237 Z= 0.381 Chirality : 0.049 0.199 3096 Planarity : 0.005 0.046 3206 Dihedral : 7.439 55.270 4306 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.88 % Favored : 94.94 % Rotamer: Outliers : 2.26 % Allowed : 15.03 % Favored : 82.71 % 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 aren not related in a simple way. whole: -0.87 (0.17), residues: 2252 helix: -0.91 (1.02), residues: 24 sheet: 0.17 (0.17), residues: 903 loop : -1.12 (0.15), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 87 TYR 0.021 0.002 TYR J 121 PHE 0.019 0.002 PHE J 422 TRP 0.016 0.002 TRP L 178 HIS 0.006 0.002 HIS G 144 Details of bonding type rmsd covalent geometry : bond 0.00595 (19059) covalent geometry : angle 0.73393 (25877) SS BOND : bond 0.00530 ( 42) SS BOND : angle 1.50719 ( 84) hydrogen bonds : bond 0.04273 ( 553) hydrogen bonds : angle 6.22327 ( 1497) link_ALPHA1-2 : bond 0.00407 ( 4) link_ALPHA1-2 : angle 2.36237 ( 12) link_ALPHA1-3 : bond 0.00612 ( 8) link_ALPHA1-3 : angle 2.26419 ( 24) link_ALPHA1-6 : bond 0.00633 ( 12) link_ALPHA1-6 : angle 1.44933 ( 36) link_BETA1-4 : bond 0.00519 ( 40) link_BETA1-4 : angle 1.95629 ( 120) link_BETA1-6 : bond 0.01157 ( 4) link_BETA1-6 : angle 1.20824 ( 12) link_NAG-ASN : bond 0.00551 ( 24) link_NAG-ASN : angle 2.72302 ( 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 185 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7382 (m-70) REVERT: E 23 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8298 (mtpp) REVERT: E 86 LEU cc_start: 0.7992 (mt) cc_final: 0.7557 (mp) REVERT: F 24 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8198 (ttp-110) REVERT: F 61 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7457 (mtm110) REVERT: F 93 ASN cc_start: 0.8983 (m-40) cc_final: 0.8265 (t0) REVERT: F 109 ARG cc_start: 0.8454 (ptm160) cc_final: 0.6537 (ptp-170) REVERT: J 362 MET cc_start: 0.8641 (ptp) cc_final: 0.8305 (ptt) REVERT: A 10 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 73 ASP cc_start: 0.7434 (t0) cc_final: 0.7144 (t0) REVERT: A 86 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (pt) REVERT: A 102 ASP cc_start: 0.8998 (p0) cc_final: 0.8722 (p0) REVERT: D 1 GLU cc_start: 0.7360 (tt0) cc_final: 0.6859 (tm-30) REVERT: D 3 VAL cc_start: 0.9370 (t) cc_final: 0.9042 (m) REVERT: D 11 LEU cc_start: 0.8677 (tp) cc_final: 0.8204 (mm) REVERT: D 24 ARG cc_start: 0.7812 (ppp80) cc_final: 0.7429 (ppp80) REVERT: D 37 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: D 93 ASN cc_start: 0.8925 (m-40) cc_final: 0.8166 (t0) REVERT: D 109 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7374 (pmt170) REVERT: K 119 GLU cc_start: 0.8900 (mp0) cc_final: 0.8567 (mp0) REVERT: C 13 GLU cc_start: 0.8676 (mp0) cc_final: 0.8158 (pm20) REVERT: C 23 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8921 (mtpm) REVERT: C 65 GLN cc_start: 0.8161 (tt0) cc_final: 0.7635 (mm-40) REVERT: C 102 ASP cc_start: 0.9071 (p0) cc_final: 0.8819 (p0) REVERT: C 120 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7072 (pp30) REVERT: I 13 LEU cc_start: 0.9040 (mt) cc_final: 0.8610 (tm) REVERT: I 24 ARG cc_start: 0.6705 (tmm-80) cc_final: 0.6335 (tmm160) REVERT: I 35 TRP cc_start: 0.8047 (m100) cc_final: 0.6767 (m100) REVERT: I 75 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8759 (tp) REVERT: I 88 CYS cc_start: 0.7212 (p) cc_final: 0.6545 (p) outliers start: 44 outliers final: 23 residues processed: 174 average time/residue: 0.7751 time to fit residues: 149.0676 Evaluate side-chains 165 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 75 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain D residue 14 SER 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 148 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 L residue 465 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 215 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN G 294 ASN G 441 ASN E 62 GLN J 226 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.094669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065745 restraints weight = 37721.060| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.24 r_work: 0.2909 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19193 Z= 0.142 Angle : 0.693 11.812 26237 Z= 0.343 Chirality : 0.046 0.189 3096 Planarity : 0.004 0.049 3206 Dihedral : 6.934 50.392 4306 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 2.01 % Allowed : 15.44 % 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 aren not related in a simple way. whole: -0.75 (0.17), residues: 2252 helix: -0.82 (1.04), residues: 24 sheet: 0.22 (0.17), residues: 913 loop : -1.03 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 87 TYR 0.019 0.001 TYR F 49 PHE 0.015 0.002 PHE G 410 TRP 0.020 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 Details of bonding type rmsd covalent geometry : bond 0.00327 (19059) covalent geometry : angle 0.66661 (25877) SS BOND : bond 0.00409 ( 42) SS BOND : angle 1.29549 ( 84) hydrogen bonds : bond 0.03610 ( 553) hydrogen bonds : angle 6.03295 ( 1497) link_ALPHA1-2 : bond 0.00504 ( 4) link_ALPHA1-2 : angle 2.33910 ( 12) link_ALPHA1-3 : bond 0.00951 ( 8) link_ALPHA1-3 : angle 1.83232 ( 24) link_ALPHA1-6 : bond 0.00717 ( 12) link_ALPHA1-6 : angle 1.33250 ( 36) link_BETA1-4 : bond 0.00504 ( 40) link_BETA1-4 : angle 1.64449 ( 120) link_BETA1-6 : bond 0.01071 ( 4) link_BETA1-6 : angle 1.28464 ( 12) link_NAG-ASN : bond 0.00336 ( 24) link_NAG-ASN : angle 2.33693 ( 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 180 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7416 (m-70) REVERT: E 23 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8324 (mtpp) REVERT: E 86 LEU cc_start: 0.8031 (mt) cc_final: 0.7658 (mp) REVERT: F 24 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8159 (ttp-110) REVERT: F 93 ASN cc_start: 0.8860 (m-40) cc_final: 0.8122 (t0) REVERT: F 109 ARG cc_start: 0.8436 (ptm160) cc_final: 0.6563 (ptp-170) REVERT: J 362 MET cc_start: 0.8471 (ptp) cc_final: 0.8111 (ptt) REVERT: A 10 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 23 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8352 (mmmt) REVERT: A 73 ASP cc_start: 0.7257 (t0) cc_final: 0.6984 (t0) REVERT: A 86 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7346 (pt) REVERT: A 102 ASP cc_start: 0.8879 (p0) cc_final: 0.8582 (p0) REVERT: D 1 GLU cc_start: 0.7178 (tt0) cc_final: 0.6809 (tm-30) REVERT: D 3 VAL cc_start: 0.9376 (t) cc_final: 0.9064 (m) REVERT: D 11 LEU cc_start: 0.8680 (tp) cc_final: 0.8199 (mm) REVERT: D 24 ARG cc_start: 0.7721 (ppp80) cc_final: 0.7384 (ppp80) REVERT: D 37 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: D 93 ASN cc_start: 0.8777 (m-40) cc_final: 0.7986 (t0) REVERT: D 109 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7438 (pmt170) REVERT: K 119 GLU cc_start: 0.8766 (mp0) cc_final: 0.8365 (mp0) REVERT: C 13 GLU cc_start: 0.8632 (mp0) cc_final: 0.8120 (pm20) REVERT: C 23 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8889 (mtpm) REVERT: C 46 GLU cc_start: 0.7700 (tt0) cc_final: 0.7291 (tt0) REVERT: C 65 GLN cc_start: 0.7933 (tt0) cc_final: 0.7451 (mm-40) REVERT: C 102 ASP cc_start: 0.9004 (p0) cc_final: 0.8699 (p0) REVERT: I 4 MET cc_start: 0.8108 (mmm) cc_final: 0.7239 (mmm) REVERT: I 13 LEU cc_start: 0.9089 (mt) cc_final: 0.8664 (tm) REVERT: I 24 ARG cc_start: 0.6709 (tmm-80) cc_final: 0.6305 (tmm160) REVERT: I 35 TRP cc_start: 0.7921 (m100) cc_final: 0.6591 (m100) REVERT: I 75 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8824 (tp) REVERT: I 88 CYS cc_start: 0.6598 (p) cc_final: 0.5999 (p) outliers start: 39 outliers final: 21 residues processed: 170 average time/residue: 0.7605 time to fit residues: 143.4050 Evaluate side-chains 161 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 294 ASN 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 E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 128 LYS 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 A residue 122 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 148 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 C residue 23 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 117 optimal weight: 0.1980 chunk 193 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN G 294 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN J 226 GLN J 441 ASN A 3 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065054 restraints weight = 37775.017| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.22 r_work: 0.2893 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19193 Z= 0.192 Angle : 0.728 12.282 26237 Z= 0.362 Chirality : 0.047 0.193 3096 Planarity : 0.004 0.062 3206 Dihedral : 7.054 51.634 4306 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 1.60 % Allowed : 15.90 % Favored : 82.50 % 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 aren not related in a simple way. whole: -0.84 (0.17), residues: 2252 helix: -0.84 (1.03), residues: 24 sheet: 0.16 (0.17), residues: 913 loop : -1.09 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 87 TYR 0.027 0.002 TYR A 80 PHE 0.017 0.002 PHE G 410 TRP 0.016 0.001 TRP L 178 HIS 0.004 0.001 HIS G 144 Details of bonding type rmsd covalent geometry : bond 0.00455 (19059) covalent geometry : angle 0.70110 (25877) SS BOND : bond 0.00446 ( 42) SS BOND : angle 1.35778 ( 84) hydrogen bonds : bond 0.03858 ( 553) hydrogen bonds : angle 6.05870 ( 1497) link_ALPHA1-2 : bond 0.00483 ( 4) link_ALPHA1-2 : angle 2.34617 ( 12) link_ALPHA1-3 : bond 0.00769 ( 8) link_ALPHA1-3 : angle 2.00490 ( 24) link_ALPHA1-6 : bond 0.00672 ( 12) link_ALPHA1-6 : angle 1.37998 ( 36) link_BETA1-4 : bond 0.00501 ( 40) link_BETA1-4 : angle 1.72837 ( 120) link_BETA1-6 : bond 0.01092 ( 4) link_BETA1-6 : angle 1.23868 ( 12) link_NAG-ASN : bond 0.00419 ( 24) link_NAG-ASN : angle 2.46799 ( 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 166 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7410 (m-70) REVERT: E 23 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8301 (mtpp) REVERT: E 86 LEU cc_start: 0.7992 (mt) cc_final: 0.7566 (mp) REVERT: F 24 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8204 (ttp-110) REVERT: F 93 ASN cc_start: 0.9017 (m-40) cc_final: 0.8244 (t0) REVERT: F 109 ARG cc_start: 0.8426 (ptm160) cc_final: 0.6539 (ptp-170) REVERT: J 362 MET cc_start: 0.8590 (ptp) cc_final: 0.8249 (ptt) REVERT: A 10 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 73 ASP cc_start: 0.7408 (t0) cc_final: 0.7139 (t0) REVERT: A 102 ASP cc_start: 0.8994 (p0) cc_final: 0.8696 (p0) REVERT: D 1 GLU cc_start: 0.7350 (tt0) cc_final: 0.6810 (tm-30) REVERT: D 3 VAL cc_start: 0.9379 (t) cc_final: 0.9073 (m) REVERT: D 4 MET cc_start: 0.7763 (mtp) cc_final: 0.7327 (mmm) REVERT: D 11 LEU cc_start: 0.8676 (tp) cc_final: 0.8206 (mm) REVERT: D 24 ARG cc_start: 0.7776 (ppp80) cc_final: 0.7273 (ppp80) REVERT: D 37 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: D 81 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8058 (tp30) REVERT: D 93 ASN cc_start: 0.8903 (m-40) cc_final: 0.8133 (t0) REVERT: D 109 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7376 (pmt170) REVERT: K 119 GLU cc_start: 0.8887 (mp0) cc_final: 0.8497 (mp0) REVERT: C 13 GLU cc_start: 0.8661 (mp0) cc_final: 0.8167 (pm20) REVERT: C 23 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8925 (mtpm) REVERT: C 46 GLU cc_start: 0.7826 (tt0) cc_final: 0.7436 (tt0) REVERT: C 65 GLN cc_start: 0.8021 (tt0) cc_final: 0.7528 (mm-40) REVERT: C 102 ASP cc_start: 0.9086 (p0) cc_final: 0.8792 (p0) REVERT: I 13 LEU cc_start: 0.9078 (mt) cc_final: 0.8653 (tm) REVERT: I 24 ARG cc_start: 0.6705 (tmm-80) cc_final: 0.6337 (tmm160) REVERT: I 35 TRP cc_start: 0.8067 (m100) cc_final: 0.6776 (m100) REVERT: I 75 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8540 (tp) REVERT: I 88 CYS cc_start: 0.7218 (p) cc_final: 0.6627 (p) outliers start: 31 outliers final: 20 residues processed: 159 average time/residue: 0.7728 time to fit residues: 136.0438 Evaluate side-chains 156 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 128 LYS 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 122 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 148 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 C residue 23 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 131 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 226 GLN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN A 3 HIS ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066447 restraints weight = 37834.487| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.20 r_work: 0.2910 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19193 Z= 0.149 Angle : 0.697 11.871 26237 Z= 0.346 Chirality : 0.046 0.189 3096 Planarity : 0.004 0.050 3206 Dihedral : 6.808 48.878 4306 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 1.85 % Allowed : 15.75 % Favored : 82.40 % 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 aren not related in a simple way. whole: -0.77 (0.17), residues: 2252 helix: -0.87 (1.02), residues: 24 sheet: 0.21 (0.17), residues: 913 loop : -1.05 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 87 TYR 0.017 0.001 TYR F 49 PHE 0.015 0.002 PHE G 410 TRP 0.020 0.001 TRP G 178 HIS 0.003 0.001 HIS G 144 Details of bonding type rmsd covalent geometry : bond 0.00346 (19059) covalent geometry : angle 0.67221 (25877) SS BOND : bond 0.00400 ( 42) SS BOND : angle 1.25568 ( 84) hydrogen bonds : bond 0.03611 ( 553) hydrogen bonds : angle 5.97685 ( 1497) link_ALPHA1-2 : bond 0.00536 ( 4) link_ALPHA1-2 : angle 2.34325 ( 12) link_ALPHA1-3 : bond 0.00881 ( 8) link_ALPHA1-3 : angle 1.83417 ( 24) link_ALPHA1-6 : bond 0.00688 ( 12) link_ALPHA1-6 : angle 1.34505 ( 36) link_BETA1-4 : bond 0.00493 ( 40) link_BETA1-4 : angle 1.60954 ( 120) link_BETA1-6 : bond 0.01036 ( 4) link_BETA1-6 : angle 1.26372 ( 12) link_NAG-ASN : bond 0.00335 ( 24) link_NAG-ASN : angle 2.30832 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6954.73 seconds wall clock time: 119 minutes 33.43 seconds (7173.43 seconds total)