Starting phenix.real_space_refine on Mon Jun 16 16:12:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3m_29704/06_2025/8g3m_29704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3m_29704/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3m_29704/06_2025/8g3m_29704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3m_29704/06_2025/8g3m_29704.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3m_29704/06_2025/8g3m_29704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3m_29704/06_2025/8g3m_29704.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.66, per 1000 atoms: 0.73 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: 7.07 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.79 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.562A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 removed outlier: 3.631A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.567A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.625A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.629A pdb=" N ALA K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.582A pdb=" N ASN K 146 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 200 Processing helix chain 'L' and resid 104 through 110 removed outlier: 3.619A pdb=" N ALA L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.575A pdb=" N ASN L 146 " --> pdb=" O VAL L 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.613A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.626A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 3.667A pdb=" N SER G 179 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.676A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.193A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.804A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.858A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.512A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.424A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.424A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.536A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.603A pdb=" N LEU F 13 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.632A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.791A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 179 through 184 removed outlier: 3.680A pdb=" N SER J 179 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.680A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.412A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.224A pdb=" N ASN J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.891A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.515A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.534A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.605A pdb=" N LEU D 13 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 96 through 102 removed outlier: 3.896A pdb=" N GLY K 96 " --> pdb=" O THR K 449 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL K 445 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS K 102 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE K 443 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG K 420 " --> pdb=" O GLY K 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 115 through 124 removed outlier: 4.753A pdb=" N TRP K 115 " --> pdb=" O THR K 138 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR K 138 " --> pdb=" O TRP K 115 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR K 157 " --> pdb=" O GLY K 135 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU K 158 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 172 " --> pdb=" O MET K 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 179 through 184 removed outlier: 3.570A pdb=" N SER K 179 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP K 213 " --> pdb=" O PHE K 205 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR K 207 " --> pdb=" O LEU K 211 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU K 211 " --> pdb=" O TYR K 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 224 through 225 removed outlier: 3.591A pdb=" N VAL K 231 " --> pdb=" O THR K 238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 224 through 225 removed outlier: 6.519A pdb=" N GLU K 258 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE K 262 " --> pdb=" O GLU K 258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 276 through 283 removed outlier: 5.474A pdb=" N GLU K 277 " --> pdb=" O ARG K 292 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG K 292 " --> pdb=" O GLU K 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 352 through 356 removed outlier: 4.684A pdb=" N TRP K 352 " --> pdb=" O GLY K 363 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY K 363 " --> pdb=" O TRP K 352 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN K 402 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N GLU K 375 " --> pdb=" O ARG K 400 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N ARG K 400 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N PHE K 377 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 13.691A pdb=" N VAL K 398 " --> pdb=" O PHE K 377 " (cutoff:3.500A) removed outlier: 15.781A pdb=" N VAL K 379 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 16.488A pdb=" N VAL K 396 " --> pdb=" O VAL K 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 96 through 102 removed outlier: 3.632A pdb=" N GLY L 96 " --> pdb=" O THR L 449 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL L 445 " --> pdb=" O PHE L 100 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS L 102 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE L 443 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG L 420 " --> pdb=" O GLY L 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 115 through 124 removed outlier: 4.783A pdb=" N TRP L 115 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR L 138 " --> pdb=" O TRP L 115 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR L 117 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN L 136 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU L 119 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU L 134 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR L 157 " --> pdb=" O GLY L 135 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU L 158 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS L 172 " --> pdb=" O MET L 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 179 through 184 removed outlier: 3.652A pdb=" N SER L 179 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP L 197 " --> pdb=" O ASN L 200 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR L 207 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU L 211 " --> pdb=" O TYR L 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 231 through 233 removed outlier: 3.708A pdb=" N VAL L 231 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU L 258 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 276 through 283 removed outlier: 5.426A pdb=" N GLU L 277 " --> pdb=" O ARG L 292 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG L 292 " --> pdb=" O GLU L 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 353 through 356 removed outlier: 7.193A pdb=" N ASN L 402 " --> pdb=" O GLY L 373 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N GLU L 375 " --> pdb=" O ARG L 400 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N ARG L 400 " --> pdb=" O GLU L 375 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N PHE L 377 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 13.798A pdb=" N VAL L 398 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 15.842A pdb=" N VAL L 379 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 16.487A pdb=" N VAL L 396 " --> pdb=" O VAL L 379 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.543A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.593A pdb=" N LEU I 13 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 8.17 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 469 or resid 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: 4.150 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: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.250 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (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 TRP 0.086 0.014 TRP K 115 HIS 0.033 0.007 HIS K 168 PHE 0.063 0.012 PHE K 205 TYR 0.077 0.014 TYR J 121 ARG 0.027 0.003 ARG K 156 Details of bonding type rmsd link_NAG-ASN : bond 0.01934 ( 24) link_NAG-ASN : angle 6.29874 ( 72) 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_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) hydrogen bonds : bond 0.15792 ( 553) hydrogen bonds : angle 8.42271 ( 1497) link_BETA1-6 : bond 0.02248 ( 4) link_BETA1-6 : angle 4.71179 ( 12) SS BOND : bond 0.06623 ( 42) SS BOND : angle 2.27860 ( 84) covalent geometry : bond 0.01631 (19059) covalent geometry : angle 1.78776 (25877) *********************** 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 : 2.051 Fit side-chains revert: symmetry clash 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 93 ASN cc_start: 0.8666 (m-40) cc_final: 0.8242 (t0) REVERT: F 108 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8724 (tmmt) REVERT: F 109 ARG cc_start: 0.7843 (ptm160) cc_final: 0.5761 (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: 0.8145 (mp) REVERT: D 14 SER cc_start: 0.6749 (m) cc_final: 0.6208 (t) REVERT: D 50 ASP cc_start: 0.9250 (m-30) cc_final: 0.8644 (p0) REVERT: D 93 ASN cc_start: 0.8717 (m-40) cc_final: 0.8455 (t0) REVERT: D 104 LYS cc_start: 0.9142 (tttt) cc_final: 0.8942 (tmtm) 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: 0.7862 (tp30) REVERT: I 11 LEU cc_start: 0.9166 (tp) cc_final: 0.8924 (tt) REVERT: I 13 LEU cc_start: 0.8531 (mt) cc_final: 0.8285 (tm) REVERT: I 106 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8163 (tm-30) outliers start: 4 outliers final: 1 residues processed: 285 average time/residue: 1.3966 time to fit residues: 443.0313 Evaluate side-chains 149 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.097624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067872 restraints weight = 36758.000| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.23 r_work: 0.2930 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19193 Z= 0.154 Angle : 0.785 9.243 26237 Z= 0.388 Chirality : 0.049 0.170 3096 Planarity : 0.004 0.044 3206 Dihedral : 13.017 79.732 4308 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.71 % Favored : 97.11 % Rotamer: Outliers : 2.06 % Allowed : 9.52 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2252 helix: -0.63 (0.81), residues: 24 sheet: 0.11 (0.16), residues: 983 loop : -0.80 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 178 HIS 0.004 0.001 HIS K 264 PHE 0.017 0.002 PHE L 354 TYR 0.015 0.002 TYR G 121 ARG 0.009 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 24) link_NAG-ASN : angle 3.04200 ( 72) link_ALPHA1-6 : bond 0.00864 ( 12) link_ALPHA1-6 : angle 1.53907 ( 36) link_BETA1-4 : bond 0.00656 ( 40) link_BETA1-4 : angle 2.82771 ( 120) link_ALPHA1-2 : bond 0.00723 ( 4) link_ALPHA1-2 : angle 1.77678 ( 12) link_ALPHA1-3 : bond 0.01114 ( 8) link_ALPHA1-3 : angle 2.14731 ( 24) hydrogen bonds : bond 0.04317 ( 553) hydrogen bonds : angle 6.78284 ( 1497) link_BETA1-6 : bond 0.01820 ( 4) link_BETA1-6 : angle 1.79470 ( 12) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.21094 ( 84) covalent geometry : bond 0.00327 (19059) covalent geometry : angle 0.73921 (25877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 2.214 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: 0.8242 (mm-30) cc_final: 0.8022 (mm-30) REVERT: E 80 TYR cc_start: 0.8561 (m-80) cc_final: 0.8355 (m-10) REVERT: E 86 LEU cc_start: 0.7555 (mt) cc_final: 0.7213 (mp) REVERT: E 90 ASP cc_start: 0.7845 (m-30) cc_final: 0.7591 (m-30) REVERT: F 11 LEU cc_start: 0.8928 (tp) cc_final: 0.8574 (tp) REVERT: F 17 GLU cc_start: 0.8502 (mp0) cc_final: 0.7930 (mp0) REVERT: F 93 ASN cc_start: 0.8877 (m-40) cc_final: 0.8286 (t0) REVERT: F 109 ARG cc_start: 0.8243 (ptm160) cc_final: 0.6073 (pmt170) REVERT: A 10 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7436 (mp0) REVERT: A 73 ASP cc_start: 0.7380 (t0) cc_final: 0.7048 (t0) REVERT: A 81 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7296 (ttp) REVERT: D 1 GLU cc_start: 0.7167 (tt0) cc_final: 0.6865 (mm-30) REVERT: D 11 LEU cc_start: 0.8551 (tp) cc_final: 0.8050 (mp) REVERT: D 50 ASP cc_start: 0.8934 (m-30) cc_final: 0.8223 (p0) REVERT: D 93 ASN cc_start: 0.8668 (m-40) cc_final: 0.8313 (t0) REVERT: D 104 LYS cc_start: 0.9191 (tttt) cc_final: 0.8926 (tmtm) REVERT: K 119 GLU cc_start: 0.8863 (mp0) cc_final: 0.8587 (mp0) REVERT: C 13 GLU cc_start: 0.8485 (mp0) cc_final: 0.7979 (pm20) REVERT: C 29 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: C 65 GLN cc_start: 0.7952 (tt0) cc_final: 0.7359 (mm110) REVERT: I 11 LEU cc_start: 0.9014 (tp) cc_final: 0.8682 (tt) REVERT: I 13 LEU cc_start: 0.8798 (mt) cc_final: 0.8317 (tm) REVERT: I 93 ASN cc_start: 0.8561 (m-40) cc_final: 0.8158 (t0) REVERT: I 106 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7729 (tm-30) outliers start: 40 outliers final: 15 residues processed: 206 average time/residue: 1.4926 time to fit residues: 342.9494 Evaluate side-chains 163 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 21 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain 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 C residue 29 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 127 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** J 441 ASN A 62 GLN K 294 ASN K 441 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069506 restraints weight = 36913.211| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.24 r_work: 0.2965 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19193 Z= 0.125 Angle : 0.706 13.492 26237 Z= 0.344 Chirality : 0.047 0.220 3096 Planarity : 0.004 0.039 3206 Dihedral : 9.862 63.338 4306 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 11.99 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2252 helix: -0.66 (0.91), residues: 24 sheet: 0.37 (0.17), residues: 937 loop : -0.65 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 178 HIS 0.004 0.001 HIS C 3 PHE 0.013 0.002 PHE K 410 TYR 0.016 0.001 TYR G 121 ARG 0.009 0.000 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 24) link_NAG-ASN : angle 2.54048 ( 72) link_ALPHA1-6 : bond 0.00831 ( 12) link_ALPHA1-6 : angle 1.34483 ( 36) link_BETA1-4 : bond 0.00672 ( 40) link_BETA1-4 : angle 2.44465 ( 120) link_ALPHA1-2 : bond 0.00739 ( 4) link_ALPHA1-2 : angle 1.93621 ( 12) link_ALPHA1-3 : bond 0.00998 ( 8) link_ALPHA1-3 : angle 1.46352 ( 24) hydrogen bonds : bond 0.03593 ( 553) hydrogen bonds : angle 6.28661 ( 1497) link_BETA1-6 : bond 0.01318 ( 4) link_BETA1-6 : angle 1.36296 ( 12) SS BOND : bond 0.00485 ( 42) SS BOND : angle 1.46551 ( 84) covalent geometry : bond 0.00260 (19059) covalent geometry : angle 0.66752 (25877) *********************** 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 212 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 3.275 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 23 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7801 (mtpp) REVERT: E 80 TYR cc_start: 0.8633 (m-80) cc_final: 0.8409 (m-10) REVERT: E 86 LEU cc_start: 0.7747 (mt) cc_final: 0.7406 (mp) REVERT: F 61 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7011 (mtm110) REVERT: F 93 ASN cc_start: 0.8808 (m-40) cc_final: 0.8204 (t0) REVERT: F 109 ARG cc_start: 0.8619 (ptm160) cc_final: 0.6785 (pmt170) REVERT: J 362 MET cc_start: 0.8355 (ptp) cc_final: 0.7972 (ptt) REVERT: A 10 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7515 (mp0) REVERT: A 46 GLU cc_start: 0.7134 (tt0) cc_final: 0.6920 (tt0) REVERT: A 73 ASP cc_start: 0.7420 (t0) cc_final: 0.7173 (t0) REVERT: A 81 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7237 (ttp) REVERT: A 107 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: D 1 GLU cc_start: 0.7043 (tt0) cc_final: 0.6820 (mm-30) REVERT: D 3 VAL cc_start: 0.9201 (t) cc_final: 0.8900 (m) REVERT: D 11 LEU cc_start: 0.8637 (tp) cc_final: 0.7984 (mp) REVERT: D 18 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7317 (tpt-90) REVERT: D 93 ASN cc_start: 0.8656 (m-40) cc_final: 0.8237 (t0) REVERT: D 104 LYS cc_start: 0.9204 (tttt) cc_final: 0.8906 (tptt) REVERT: K 119 GLU cc_start: 0.8694 (mp0) cc_final: 0.8292 (mp0) REVERT: C 13 GLU cc_start: 0.8494 (mp0) cc_final: 0.7993 (pm20) REVERT: C 46 GLU cc_start: 0.7507 (tt0) cc_final: 0.7256 (tt0) REVERT: C 65 GLN cc_start: 0.7697 (tt0) cc_final: 0.7194 (mm110) REVERT: C 73 ASP cc_start: 0.6347 (t0) cc_final: 0.6004 (t0) REVERT: C 120 GLN cc_start: 0.7770 (pm20) cc_final: 0.7266 (pm20) REVERT: I 4 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7607 (mmm) REVERT: I 11 LEU cc_start: 0.9032 (tp) cc_final: 0.8482 (tt) REVERT: I 13 LEU cc_start: 0.8776 (mt) cc_final: 0.8260 (tm) REVERT: I 35 TRP cc_start: 0.7761 (m100) cc_final: 0.6516 (m100) REVERT: I 93 ASN cc_start: 0.8578 (m-40) cc_final: 0.8142 (t0) outliers start: 38 outliers final: 14 residues processed: 203 average time/residue: 1.4099 time to fit residues: 324.0170 Evaluate side-chains 164 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 10 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 88 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 K residue 230 CYS Chi-restraints excluded: chain L residue 230 CYS 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 19 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.095163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066301 restraints weight = 37765.902| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.23 r_work: 0.2898 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19193 Z= 0.203 Angle : 0.747 11.393 26237 Z= 0.367 Chirality : 0.049 0.225 3096 Planarity : 0.004 0.040 3206 Dihedral : 8.235 61.003 4306 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 2.37 % Allowed : 13.02 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2252 helix: -0.36 (1.00), residues: 24 sheet: 0.31 (0.17), residues: 961 loop : -0.79 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 178 HIS 0.005 0.001 HIS L 168 PHE 0.017 0.002 PHE J 354 TYR 0.020 0.002 TYR G 121 ARG 0.009 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 24) link_NAG-ASN : angle 2.73138 ( 72) link_ALPHA1-6 : bond 0.00733 ( 12) link_ALPHA1-6 : angle 1.53734 ( 36) link_BETA1-4 : bond 0.00544 ( 40) link_BETA1-4 : angle 2.45562 ( 120) link_ALPHA1-2 : bond 0.00504 ( 4) link_ALPHA1-2 : angle 2.19231 ( 12) link_ALPHA1-3 : bond 0.00758 ( 8) link_ALPHA1-3 : angle 2.04877 ( 24) hydrogen bonds : bond 0.04064 ( 553) hydrogen bonds : angle 6.37547 ( 1497) link_BETA1-6 : bond 0.01257 ( 4) link_BETA1-6 : angle 1.21766 ( 12) SS BOND : bond 0.00750 ( 42) SS BOND : angle 1.62683 ( 84) covalent geometry : bond 0.00476 (19059) covalent geometry : angle 0.70591 (25877) *********************** 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 204 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 229 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: E 80 TYR cc_start: 0.8633 (m-80) cc_final: 0.8416 (m-10) REVERT: E 81 MET cc_start: 0.7696 (tmm) cc_final: 0.7384 (ppp) REVERT: E 86 LEU cc_start: 0.7844 (mt) cc_final: 0.7526 (mp) REVERT: E 87 ARG cc_start: 0.7842 (mpt-90) cc_final: 0.7524 (mpp80) REVERT: F 93 ASN cc_start: 0.8815 (m-40) cc_final: 0.8131 (t0) REVERT: F 109 ARG cc_start: 0.8516 (ptm160) cc_final: 0.6636 (pmt170) REVERT: J 362 MET cc_start: 0.8438 (ptp) cc_final: 0.8059 (ptt) REVERT: A 23 LYS cc_start: 0.8589 (tptp) cc_final: 0.8274 (tppp) REVERT: A 73 ASP cc_start: 0.7441 (t0) cc_final: 0.7138 (OUTLIER) REVERT: A 107 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8807 (m-30) REVERT: D 3 VAL cc_start: 0.9281 (t) cc_final: 0.8961 (m) REVERT: D 4 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7623 (tpt) REVERT: D 11 LEU cc_start: 0.8638 (tp) cc_final: 0.8240 (mm) REVERT: D 93 ASN cc_start: 0.8727 (m-40) cc_final: 0.8162 (t0) REVERT: D 104 LYS cc_start: 0.9200 (tttt) cc_final: 0.8878 (tmtm) REVERT: K 119 GLU cc_start: 0.8795 (mp0) cc_final: 0.8398 (mp0) REVERT: K 128 LYS cc_start: 0.8355 (ptmm) cc_final: 0.7842 (ptmm) REVERT: C 13 GLU cc_start: 0.8561 (mp0) cc_final: 0.8044 (pm20) REVERT: C 29 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6717 (m-10) REVERT: C 46 GLU cc_start: 0.7639 (tt0) cc_final: 0.7238 (tt0) REVERT: C 65 GLN cc_start: 0.7855 (tt0) cc_final: 0.7385 (mm-40) REVERT: C 102 ASP cc_start: 0.8864 (p0) cc_final: 0.8599 (p0) REVERT: I 13 LEU cc_start: 0.8776 (mt) cc_final: 0.8333 (tm) REVERT: I 24 ARG cc_start: 0.6639 (tmm-80) cc_final: 0.6341 (tmm-80) REVERT: I 35 TRP cc_start: 0.7780 (m100) cc_final: 0.6495 (m100) REVERT: I 93 ASN cc_start: 0.8743 (m-40) cc_final: 0.8215 (t0) outliers start: 46 outliers final: 24 residues processed: 193 average time/residue: 1.6069 time to fit residues: 347.9814 Evaluate side-chains 174 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 4 MET 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 125 ASP 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 29 PHE Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 134 optimal weight: 0.0000 chunk 213 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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 E 43 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066909 restraints weight = 37383.651| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.15 r_work: 0.2918 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19193 Z= 0.147 Angle : 0.692 11.191 26237 Z= 0.341 Chirality : 0.046 0.191 3096 Planarity : 0.004 0.041 3206 Dihedral : 7.371 55.684 4306 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 13.18 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2252 helix: -0.49 (1.04), residues: 24 sheet: 0.35 (0.17), residues: 963 loop : -0.78 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 178 HIS 0.003 0.001 HIS C 3 PHE 0.014 0.002 PHE J 354 TYR 0.014 0.001 TYR G 121 ARG 0.007 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 24) link_NAG-ASN : angle 2.46708 ( 72) link_ALPHA1-6 : bond 0.00766 ( 12) link_ALPHA1-6 : angle 1.39114 ( 36) link_BETA1-4 : bond 0.00536 ( 40) link_BETA1-4 : angle 2.08606 ( 120) link_ALPHA1-2 : bond 0.00576 ( 4) link_ALPHA1-2 : angle 2.19077 ( 12) link_ALPHA1-3 : bond 0.00915 ( 8) link_ALPHA1-3 : angle 1.80534 ( 24) hydrogen bonds : bond 0.03654 ( 553) hydrogen bonds : angle 6.21070 ( 1497) link_BETA1-6 : bond 0.01180 ( 4) link_BETA1-6 : angle 1.26235 ( 12) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.40841 ( 84) covalent geometry : bond 0.00340 (19059) covalent geometry : angle 0.65878 (25877) *********************** 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 204 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 229 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: E 80 TYR cc_start: 0.8702 (m-80) cc_final: 0.8484 (m-10) REVERT: E 81 MET cc_start: 0.7734 (tmm) cc_final: 0.7428 (ppp) REVERT: E 86 LEU cc_start: 0.7830 (mt) cc_final: 0.7469 (mp) REVERT: F 24 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7933 (ttp-110) REVERT: F 82 ASP cc_start: 0.7632 (m-30) cc_final: 0.7407 (m-30) REVERT: F 93 ASN cc_start: 0.8959 (m-40) cc_final: 0.8314 (t0) REVERT: F 109 ARG cc_start: 0.8555 (ptm160) cc_final: 0.6391 (ptp-170) REVERT: A 73 ASP cc_start: 0.7345 (t0) cc_final: 0.7124 (OUTLIER) REVERT: A 102 ASP cc_start: 0.9067 (p0) cc_final: 0.8842 (p0) REVERT: A 107 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8914 (m-30) REVERT: D 3 VAL cc_start: 0.9299 (t) cc_final: 0.8980 (m) REVERT: D 4 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7700 (tpt) REVERT: D 11 LEU cc_start: 0.8636 (tp) cc_final: 0.8238 (mm) REVERT: D 93 ASN cc_start: 0.8847 (m-40) cc_final: 0.8279 (t0) REVERT: D 104 LYS cc_start: 0.9216 (tttt) cc_final: 0.8871 (tmtm) REVERT: K 119 GLU cc_start: 0.8806 (mp0) cc_final: 0.8464 (mp0) REVERT: K 261 LYS cc_start: 0.6638 (tptt) cc_final: 0.6396 (tttm) REVERT: C 10 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7492 (tm-30) REVERT: C 13 GLU cc_start: 0.8615 (mp0) cc_final: 0.8054 (pm20) REVERT: C 46 GLU cc_start: 0.7833 (tt0) cc_final: 0.7488 (tt0) REVERT: C 65 GLN cc_start: 0.7815 (tt0) cc_final: 0.7337 (mm-40) REVERT: C 73 ASP cc_start: 0.6686 (t0) cc_final: 0.6264 (t0) REVERT: C 102 ASP cc_start: 0.9008 (p0) cc_final: 0.8721 (p0) REVERT: I 4 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7655 (mmm) REVERT: I 13 LEU cc_start: 0.8946 (mt) cc_final: 0.8444 (tm) REVERT: I 24 ARG cc_start: 0.6651 (tmm-80) cc_final: 0.6273 (tmm-80) REVERT: I 35 TRP cc_start: 0.8020 (m100) cc_final: 0.6734 (m100) REVERT: I 93 ASN cc_start: 0.8847 (m-40) cc_final: 0.8613 (p0) outliers start: 50 outliers final: 26 residues processed: 193 average time/residue: 1.4324 time to fit residues: 309.6278 Evaluate side-chains 170 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 GLU 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 10 THR Chi-restraints excluded: chain F residue 13 LEU 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 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 4 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR 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 28 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 0.0370 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.0060 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.9276 ------------------------------------------------------------------------------- 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** J 441 ASN K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.067482 restraints weight = 37831.674| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.25 r_work: 0.2916 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19193 Z= 0.138 Angle : 0.674 10.795 26237 Z= 0.333 Chirality : 0.046 0.187 3096 Planarity : 0.004 0.042 3206 Dihedral : 6.992 52.163 4306 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 2.47 % Allowed : 13.28 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2252 helix: -0.65 (1.02), residues: 24 sheet: 0.36 (0.17), residues: 943 loop : -0.73 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.004 0.001 HIS G 336 PHE 0.013 0.002 PHE J 354 TYR 0.014 0.001 TYR G 121 ARG 0.010 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 24) link_NAG-ASN : angle 2.35935 ( 72) link_ALPHA1-6 : bond 0.00748 ( 12) link_ALPHA1-6 : angle 1.36148 ( 36) link_BETA1-4 : bond 0.00517 ( 40) link_BETA1-4 : angle 1.88930 ( 120) link_ALPHA1-2 : bond 0.00592 ( 4) link_ALPHA1-2 : angle 2.18105 ( 12) link_ALPHA1-3 : bond 0.00908 ( 8) link_ALPHA1-3 : angle 1.74328 ( 24) hydrogen bonds : bond 0.03498 ( 553) hydrogen bonds : angle 6.09702 ( 1497) link_BETA1-6 : bond 0.01105 ( 4) link_BETA1-6 : angle 1.24623 ( 12) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.27714 ( 84) covalent geometry : bond 0.00316 (19059) covalent geometry : angle 0.64406 (25877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 2.135 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: G 229 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: E 80 TYR cc_start: 0.8713 (m-80) cc_final: 0.8492 (m-10) REVERT: E 81 MET cc_start: 0.7695 (tmm) cc_final: 0.7376 (ppp) REVERT: E 86 LEU cc_start: 0.7874 (mt) cc_final: 0.7486 (mp) REVERT: F 24 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8018 (ttp-110) REVERT: F 61 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7250 (mtm110) REVERT: F 93 ASN cc_start: 0.8831 (m-40) cc_final: 0.8145 (t0) REVERT: F 109 ARG cc_start: 0.8537 (ptm160) cc_final: 0.6491 (ptp-170) REVERT: J 128 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7532 (ptmt) REVERT: A 73 ASP cc_start: 0.7357 (t0) cc_final: 0.7069 (t0) REVERT: A 102 ASP cc_start: 0.8990 (p0) cc_final: 0.8739 (p0) REVERT: D 3 VAL cc_start: 0.9352 (t) cc_final: 0.9067 (m) REVERT: D 11 LEU cc_start: 0.8680 (tp) cc_final: 0.8241 (mm) REVERT: D 24 ARG cc_start: 0.7557 (ppp80) cc_final: 0.7229 (ppp80) REVERT: D 93 ASN cc_start: 0.8729 (m-40) cc_final: 0.7998 (t0) REVERT: D 104 LYS cc_start: 0.9213 (tttt) cc_final: 0.8877 (tmtm) REVERT: K 119 GLU cc_start: 0.8674 (mp0) cc_final: 0.8312 (mp0) REVERT: K 261 LYS cc_start: 0.6621 (tptt) cc_final: 0.6417 (tttm) REVERT: C 13 GLU cc_start: 0.8602 (mp0) cc_final: 0.8057 (pm20) REVERT: C 46 GLU cc_start: 0.7729 (tt0) cc_final: 0.7371 (tt0) REVERT: C 65 GLN cc_start: 0.7763 (tt0) cc_final: 0.7303 (mm-40) REVERT: C 102 ASP cc_start: 0.8919 (p0) cc_final: 0.8600 (p0) REVERT: I 4 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: I 6 GLN cc_start: 0.7338 (tt0) cc_final: 0.6977 (pt0) REVERT: I 13 LEU cc_start: 0.9026 (mt) cc_final: 0.8588 (tm) REVERT: I 24 ARG cc_start: 0.6585 (tmm-80) cc_final: 0.6267 (tmm-80) REVERT: I 35 TRP cc_start: 0.7838 (m100) cc_final: 0.6484 (m100) REVERT: I 75 ILE cc_start: 0.9115 (mt) cc_final: 0.8732 (tp) REVERT: I 101 GLN cc_start: 0.8441 (pm20) cc_final: 0.8171 (pm20) outliers start: 48 outliers final: 27 residues processed: 195 average time/residue: 1.4143 time to fit residues: 308.6392 Evaluate side-chains 165 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 GLU 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 128 LYS Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 228 SER 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 76 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 200 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 226 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066359 restraints weight = 37400.973| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.23 r_work: 0.2921 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19193 Z= 0.152 Angle : 0.684 10.663 26237 Z= 0.339 Chirality : 0.046 0.191 3096 Planarity : 0.004 0.045 3206 Dihedral : 6.872 50.171 4306 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 2.32 % Allowed : 13.43 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2252 helix: -0.59 (1.04), residues: 24 sheet: 0.36 (0.17), residues: 935 loop : -0.73 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 178 HIS 0.003 0.001 HIS G 144 PHE 0.015 0.002 PHE J 354 TYR 0.015 0.001 TYR G 121 ARG 0.014 0.000 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 24) link_NAG-ASN : angle 2.38001 ( 72) link_ALPHA1-6 : bond 0.00718 ( 12) link_ALPHA1-6 : angle 1.36555 ( 36) link_BETA1-4 : bond 0.00505 ( 40) link_BETA1-4 : angle 1.77607 ( 120) link_ALPHA1-2 : bond 0.00549 ( 4) link_ALPHA1-2 : angle 2.21423 ( 12) link_ALPHA1-3 : bond 0.00872 ( 8) link_ALPHA1-3 : angle 1.81503 ( 24) hydrogen bonds : bond 0.03575 ( 553) hydrogen bonds : angle 6.00234 ( 1497) link_BETA1-6 : bond 0.01101 ( 4) link_BETA1-6 : angle 1.23249 ( 12) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.21987 ( 84) covalent geometry : bond 0.00354 (19059) covalent geometry : angle 0.65589 (25877) *********************** 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 197 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 2.155 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: G 229 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: G 431 LYS cc_start: 0.8187 (tptp) cc_final: 0.7968 (tppt) REVERT: E 80 TYR cc_start: 0.8756 (m-80) cc_final: 0.8544 (m-10) REVERT: E 81 MET cc_start: 0.7744 (tmm) cc_final: 0.7424 (ppp) REVERT: E 86 LEU cc_start: 0.7922 (mt) cc_final: 0.7536 (mp) REVERT: F 17 GLU cc_start: 0.8618 (mp0) cc_final: 0.8312 (mp0) REVERT: F 24 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8150 (ttp-110) REVERT: F 61 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7429 (mtm110) REVERT: F 82 ASP cc_start: 0.7784 (m-30) cc_final: 0.7549 (m-30) REVERT: F 93 ASN cc_start: 0.8972 (m-40) cc_final: 0.8248 (t0) REVERT: F 109 ARG cc_start: 0.8533 (ptm160) cc_final: 0.6567 (ptp-170) REVERT: A 10 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 73 ASP cc_start: 0.7455 (t0) cc_final: 0.7187 (t0) REVERT: A 81 MET cc_start: 0.7807 (tmm) cc_final: 0.6946 (ttp) REVERT: A 102 ASP cc_start: 0.9086 (p0) cc_final: 0.8841 (p0) REVERT: D 3 VAL cc_start: 0.9376 (t) cc_final: 0.9093 (m) REVERT: D 11 LEU cc_start: 0.8641 (tp) cc_final: 0.8183 (mm) REVERT: D 24 ARG cc_start: 0.7540 (ppp80) cc_final: 0.7202 (ppp80) REVERT: D 93 ASN cc_start: 0.8857 (m-40) cc_final: 0.8116 (t0) REVERT: D 104 LYS cc_start: 0.9212 (tttt) cc_final: 0.8865 (tmtm) REVERT: D 109 ARG cc_start: 0.7820 (ptm160) cc_final: 0.7383 (pmt170) REVERT: K 119 GLU cc_start: 0.8867 (mp0) cc_final: 0.8507 (mp0) REVERT: K 150 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7993 (mtm110) REVERT: K 261 LYS cc_start: 0.6643 (tptt) cc_final: 0.6399 (tttm) REVERT: C 13 GLU cc_start: 0.8637 (mp0) cc_final: 0.8097 (pm20) REVERT: C 46 GLU cc_start: 0.7895 (tt0) cc_final: 0.7572 (tt0) REVERT: C 65 GLN cc_start: 0.7838 (tt0) cc_final: 0.7356 (mm-40) REVERT: C 73 ASP cc_start: 0.6734 (t0) cc_final: 0.6046 (t0) REVERT: C 102 ASP cc_start: 0.9029 (p0) cc_final: 0.8742 (p0) REVERT: I 4 MET cc_start: 0.8218 (mmm) cc_final: 0.7461 (mmm) REVERT: I 13 LEU cc_start: 0.9020 (mt) cc_final: 0.8580 (tm) REVERT: I 24 ARG cc_start: 0.6664 (tmm-80) cc_final: 0.6333 (tmm-80) REVERT: I 35 TRP cc_start: 0.8018 (m100) cc_final: 0.6729 (m100) REVERT: I 75 ILE cc_start: 0.9139 (mt) cc_final: 0.8747 (tp) REVERT: I 88 CYS cc_start: 0.7274 (p) cc_final: 0.6559 (p) REVERT: I 101 GLN cc_start: 0.8556 (pm20) cc_final: 0.8268 (pm20) outliers start: 45 outliers final: 23 residues processed: 189 average time/residue: 1.4225 time to fit residues: 300.1598 Evaluate side-chains 168 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 GLU 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 228 SER 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 J residue 390 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 155 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 226 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.093120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064676 restraints weight = 37602.488| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.05 r_work: 0.2903 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19193 Z= 0.247 Angle : 0.765 11.853 26237 Z= 0.381 Chirality : 0.049 0.203 3096 Planarity : 0.005 0.046 3206 Dihedral : 7.441 55.508 4306 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 2.06 % Allowed : 14.41 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2252 helix: -0.74 (1.00), residues: 24 sheet: 0.24 (0.17), residues: 921 loop : -1.03 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 178 HIS 0.006 0.002 HIS G 144 PHE 0.019 0.003 PHE J 422 TYR 0.020 0.002 TYR G 121 ARG 0.012 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 24) link_NAG-ASN : angle 2.71035 ( 72) link_ALPHA1-6 : bond 0.00639 ( 12) link_ALPHA1-6 : angle 1.45698 ( 36) link_BETA1-4 : bond 0.00501 ( 40) link_BETA1-4 : angle 1.93795 ( 120) link_ALPHA1-2 : bond 0.00384 ( 4) link_ALPHA1-2 : angle 2.39992 ( 12) link_ALPHA1-3 : bond 0.00609 ( 8) link_ALPHA1-3 : angle 2.28865 ( 24) hydrogen bonds : bond 0.04219 ( 553) hydrogen bonds : angle 6.18464 ( 1497) link_BETA1-6 : bond 0.01121 ( 4) link_BETA1-6 : angle 1.21873 ( 12) SS BOND : bond 0.00525 ( 42) SS BOND : angle 1.39511 ( 84) covalent geometry : bond 0.00586 (19059) covalent geometry : angle 0.73373 (25877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 MET cc_start: 0.7998 (tmm) cc_final: 0.7730 (ppp) REVERT: E 86 LEU cc_start: 0.8168 (mt) cc_final: 0.7772 (mp) REVERT: F 24 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8219 (ttp-110) REVERT: F 61 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7352 (mtm110) REVERT: F 93 ASN cc_start: 0.8955 (m-40) cc_final: 0.8342 (t0) REVERT: F 109 ARG cc_start: 0.8470 (ptm160) cc_final: 0.6610 (ptp-170) REVERT: J 362 MET cc_start: 0.8586 (ptp) cc_final: 0.8286 (ptt) REVERT: A 73 ASP cc_start: 0.7440 (t0) cc_final: 0.7134 (t0) REVERT: A 81 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7698 (ttt) REVERT: A 102 ASP cc_start: 0.9015 (p0) cc_final: 0.8768 (p0) REVERT: D 3 VAL cc_start: 0.9399 (t) cc_final: 0.9108 (m) REVERT: D 11 LEU cc_start: 0.8760 (tp) cc_final: 0.8314 (mm) REVERT: D 24 ARG cc_start: 0.7883 (ppp80) cc_final: 0.7578 (ppp80) REVERT: D 37 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: D 93 ASN cc_start: 0.8864 (m-40) cc_final: 0.8226 (t0) REVERT: D 104 LYS cc_start: 0.9164 (tttt) cc_final: 0.8879 (tmtm) REVERT: D 109 ARG cc_start: 0.7867 (ptm160) cc_final: 0.7424 (pmt170) REVERT: K 119 GLU cc_start: 0.8885 (mp0) cc_final: 0.8642 (mp0) REVERT: K 261 LYS cc_start: 0.7048 (tptt) cc_final: 0.6803 (tttm) REVERT: C 13 GLU cc_start: 0.8738 (mp0) cc_final: 0.8225 (pm20) REVERT: C 46 GLU cc_start: 0.8251 (tt0) cc_final: 0.7958 (tt0) REVERT: C 65 GLN cc_start: 0.8218 (tt0) cc_final: 0.7850 (mm-40) REVERT: C 74 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7936 (pm20) REVERT: C 102 ASP cc_start: 0.9172 (p0) cc_final: 0.8899 (p0) REVERT: I 4 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7524 (mmm) REVERT: I 13 LEU cc_start: 0.9067 (mt) cc_final: 0.8617 (tp) REVERT: I 24 ARG cc_start: 0.6654 (tmm-80) cc_final: 0.6288 (tmm160) REVERT: I 35 TRP cc_start: 0.8219 (m100) cc_final: 0.7024 (m100) REVERT: I 75 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8821 (tp) REVERT: I 88 CYS cc_start: 0.7362 (p) cc_final: 0.6727 (p) outliers start: 40 outliers final: 25 residues processed: 173 average time/residue: 1.4985 time to fit residues: 289.6898 Evaluate side-chains 163 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 228 SER 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 81 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 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 D residue 101 GLN Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 214 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064801 restraints weight = 37790.682| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.15 r_work: 0.2908 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19193 Z= 0.205 Angle : 0.737 11.622 26237 Z= 0.366 Chirality : 0.047 0.190 3096 Planarity : 0.004 0.050 3206 Dihedral : 7.336 55.028 4306 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 2.11 % Allowed : 14.51 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2252 helix: -0.82 (1.00), residues: 24 sheet: 0.10 (0.17), residues: 943 loop : -1.07 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 178 HIS 0.005 0.001 HIS G 144 PHE 0.017 0.002 PHE J 354 TYR 0.018 0.002 TYR G 121 ARG 0.012 0.001 ARG I 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 24) link_NAG-ASN : angle 2.53529 ( 72) link_ALPHA1-6 : bond 0.00673 ( 12) link_ALPHA1-6 : angle 1.37523 ( 36) link_BETA1-4 : bond 0.00500 ( 40) link_BETA1-4 : angle 1.77540 ( 120) link_ALPHA1-2 : bond 0.00430 ( 4) link_ALPHA1-2 : angle 2.45435 ( 12) link_ALPHA1-3 : bond 0.00736 ( 8) link_ALPHA1-3 : angle 2.10790 ( 24) hydrogen bonds : bond 0.03972 ( 553) hydrogen bonds : angle 6.11769 ( 1497) link_BETA1-6 : bond 0.01106 ( 4) link_BETA1-6 : angle 1.26890 ( 12) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.28808 ( 84) covalent geometry : bond 0.00485 (19059) covalent geometry : angle 0.70860 (25877) *********************** 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 185 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.8181 (p-80) cc_final: 0.7660 (m-70) REVERT: E 86 LEU cc_start: 0.8173 (mt) cc_final: 0.7756 (mp) REVERT: F 24 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8228 (ttp-110) REVERT: F 61 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7511 (mtm110) REVERT: F 93 ASN cc_start: 0.8956 (m-40) cc_final: 0.8303 (t0) REVERT: F 109 ARG cc_start: 0.8406 (ptm160) cc_final: 0.6549 (ptp-170) REVERT: A 10 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7163 (mp0) REVERT: A 23 LYS cc_start: 0.8554 (tptp) cc_final: 0.8344 (tppp) REVERT: A 73 ASP cc_start: 0.7432 (t0) cc_final: 0.7148 (t0) REVERT: A 81 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: A 102 ASP cc_start: 0.9014 (p0) cc_final: 0.8762 (p0) REVERT: D 3 VAL cc_start: 0.9371 (t) cc_final: 0.9073 (m) REVERT: D 11 LEU cc_start: 0.8758 (tp) cc_final: 0.8314 (mm) REVERT: D 24 ARG cc_start: 0.7808 (ppp80) cc_final: 0.7425 (ppp80) REVERT: D 37 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: D 81 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7996 (tp30) REVERT: D 93 ASN cc_start: 0.8870 (m-40) cc_final: 0.8201 (t0) REVERT: D 104 LYS cc_start: 0.9170 (tttt) cc_final: 0.8882 (tmtm) REVERT: D 109 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7478 (pmt170) REVERT: K 119 GLU cc_start: 0.8894 (mp0) cc_final: 0.8638 (mp0) REVERT: K 261 LYS cc_start: 0.6953 (tptt) cc_final: 0.6703 (tttt) REVERT: C 13 GLU cc_start: 0.8729 (mp0) cc_final: 0.8225 (pm20) REVERT: C 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7959 (tt0) REVERT: C 65 GLN cc_start: 0.8236 (tt0) cc_final: 0.7975 (mm-40) REVERT: C 102 ASP cc_start: 0.9177 (p0) cc_final: 0.8871 (p0) REVERT: I 4 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7525 (mmm) REVERT: I 13 LEU cc_start: 0.9062 (mt) cc_final: 0.8614 (tp) REVERT: I 24 ARG cc_start: 0.6734 (tmm-80) cc_final: 0.6405 (tmm160) REVERT: I 35 TRP cc_start: 0.8207 (m100) cc_final: 0.7032 (m100) REVERT: I 75 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (tp) REVERT: I 88 CYS cc_start: 0.7403 (p) cc_final: 0.6787 (p) outliers start: 41 outliers final: 25 residues processed: 175 average time/residue: 1.4941 time to fit residues: 293.7064 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 : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 294 ASN 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 10 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 228 SER 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 81 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 193 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 92 ASN K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066341 restraints weight = 37332.320| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.14 r_work: 0.2943 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19193 Z= 0.138 Angle : 0.695 11.122 26237 Z= 0.346 Chirality : 0.046 0.188 3096 Planarity : 0.004 0.059 3206 Dihedral : 6.912 50.470 4306 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 1.75 % Allowed : 14.98 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2252 helix: -0.69 (1.04), residues: 24 sheet: 0.22 (0.17), residues: 943 loop : -0.94 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.004 0.001 HIS K 184 PHE 0.015 0.002 PHE G 410 TYR 0.020 0.001 TYR F 49 ARG 0.014 0.000 ARG I 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 24) link_NAG-ASN : angle 2.29384 ( 72) link_ALPHA1-6 : bond 0.00704 ( 12) link_ALPHA1-6 : angle 1.34760 ( 36) link_BETA1-4 : bond 0.00527 ( 40) link_BETA1-4 : angle 1.60904 ( 120) link_ALPHA1-2 : bond 0.00537 ( 4) link_ALPHA1-2 : angle 2.38539 ( 12) link_ALPHA1-3 : bond 0.00975 ( 8) link_ALPHA1-3 : angle 1.79483 ( 24) hydrogen bonds : bond 0.03498 ( 553) hydrogen bonds : angle 6.00243 ( 1497) link_BETA1-6 : bond 0.01085 ( 4) link_BETA1-6 : angle 1.29427 ( 12) SS BOND : bond 0.00412 ( 42) SS BOND : angle 1.31237 ( 84) covalent geometry : bond 0.00318 (19059) covalent geometry : angle 0.66992 (25877) ********************** 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 175 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 2.619 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: 0.8172 (p-80) cc_final: 0.7696 (m-70) REVERT: E 86 LEU cc_start: 0.8191 (mt) cc_final: 0.7818 (mp) REVERT: F 24 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8276 (ttp-110) REVERT: F 93 ASN cc_start: 0.8936 (m-40) cc_final: 0.8294 (t0) REVERT: F 109 ARG cc_start: 0.8416 (ptm160) cc_final: 0.6622 (ptp-170) REVERT: A 10 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7122 (mp0) REVERT: A 73 ASP cc_start: 0.7416 (t0) cc_final: 0.7137 (t0) REVERT: A 81 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7670 (ttt) REVERT: A 102 ASP cc_start: 0.9004 (p0) cc_final: 0.8754 (p0) REVERT: D 3 VAL cc_start: 0.9397 (t) cc_final: 0.9115 (m) REVERT: D 11 LEU cc_start: 0.8718 (tp) cc_final: 0.8270 (mm) REVERT: D 37 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: D 81 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8020 (tp30) REVERT: D 93 ASN cc_start: 0.8825 (m-40) cc_final: 0.8150 (t0) REVERT: D 104 LYS cc_start: 0.9167 (tttt) cc_final: 0.8881 (tmtm) REVERT: D 109 ARG cc_start: 0.7735 (ptm160) cc_final: 0.7509 (pmt170) REVERT: K 119 GLU cc_start: 0.8852 (mp0) cc_final: 0.8494 (mp0) REVERT: K 261 LYS cc_start: 0.6923 (tptt) cc_final: 0.6720 (tttm) REVERT: C 13 GLU cc_start: 0.8723 (mp0) cc_final: 0.8231 (pm20) REVERT: C 46 GLU cc_start: 0.8188 (tt0) cc_final: 0.7875 (tt0) REVERT: C 65 GLN cc_start: 0.8031 (tt0) cc_final: 0.7705 (mm-40) REVERT: C 73 ASP cc_start: 0.6617 (t0) cc_final: 0.6193 (t0) REVERT: C 102 ASP cc_start: 0.9160 (p0) cc_final: 0.8851 (p0) REVERT: C 111 GLU cc_start: 0.7933 (tp30) cc_final: 0.7472 (tp30) REVERT: I 4 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: I 13 LEU cc_start: 0.9092 (mt) cc_final: 0.8684 (tm) REVERT: I 24 ARG cc_start: 0.6765 (tmm-80) cc_final: 0.6435 (tmm160) REVERT: I 35 TRP cc_start: 0.8215 (m100) cc_final: 0.7023 (m100) REVERT: I 75 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8560 (tp) REVERT: I 88 CYS cc_start: 0.7475 (p) cc_final: 0.6896 (p) outliers start: 34 outliers final: 18 residues processed: 169 average time/residue: 1.5852 time to fit residues: 299.3636 Evaluate side-chains 158 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 3 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 228 SER 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 81 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 154 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.093568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064682 restraints weight = 37745.648| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.13 r_work: 0.2904 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3721 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= 0.219 Angle : 0.754 11.801 26237 Z= 0.375 Chirality : 0.048 0.193 3096 Planarity : 0.004 0.059 3206 Dihedral : 7.274 53.813 4306 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.11 % Favored : 94.72 % Rotamer: Outliers : 1.49 % Allowed : 15.59 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2252 helix: -0.77 (1.02), residues: 24 sheet: 0.17 (0.17), residues: 927 loop : -1.10 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 178 HIS 0.005 0.001 HIS L 184 PHE 0.018 0.002 PHE G 410 TYR 0.017 0.002 TYR G 121 ARG 0.013 0.001 ARG I 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 24) link_NAG-ASN : angle 2.57675 ( 72) link_ALPHA1-6 : bond 0.00623 ( 12) link_ALPHA1-6 : angle 1.43202 ( 36) link_BETA1-4 : bond 0.00503 ( 40) link_BETA1-4 : angle 1.81261 ( 120) link_ALPHA1-2 : bond 0.00392 ( 4) link_ALPHA1-2 : angle 2.40754 ( 12) link_ALPHA1-3 : bond 0.00691 ( 8) link_ALPHA1-3 : angle 2.17978 ( 24) hydrogen bonds : bond 0.04065 ( 553) hydrogen bonds : angle 6.11172 ( 1497) link_BETA1-6 : bond 0.01088 ( 4) link_BETA1-6 : angle 1.23055 ( 12) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.54434 ( 84) covalent geometry : bond 0.00518 (19059) covalent geometry : angle 0.72439 (25877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14526.55 seconds wall clock time: 252 minutes 15.72 seconds (15135.72 seconds total)