Starting phenix.real_space_refine on Mon May 19 18:09:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3m_29704/05_2025/8g3m_29704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3m_29704/05_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_29704/05_2025/8g3m_29704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3m_29704/05_2025/8g3m_29704.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3m_29704/05_2025/8g3m_29704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3m_29704/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 11.32, per 1000 atoms: 0.61 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: 5.59 Conformation dependent library (CDL) restraints added in 2.3 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: 2.70 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: 6.69 Time building geometry restraints manager: 6.36 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: 3.200 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: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 43.840 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.450 ------------------------------------------------------------------------------- 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 : 1.999 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: 1.4065 time to fit residues: 445.9736 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 : 2.025 ------------------------------------------------------------------------------- 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 = 0.067873 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: 0.2791 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 1.959 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: 0.7844 (m-30) cc_final: 0.7592 (m-30) REVERT: F 11 LEU cc_start: 0.8929 (tp) cc_final: 0.8573 (tp) REVERT: F 17 GLU cc_start: 0.8502 (mp0) cc_final: 0.7930 (mp0) REVERT: F 93 ASN cc_start: 0.8876 (m-40) cc_final: 0.8284 (t0) REVERT: F 109 ARG cc_start: 0.8243 (ptm160) cc_final: 0.6074 (pmt170) REVERT: A 10 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7437 (mp0) REVERT: A 73 ASP cc_start: 0.7382 (t0) cc_final: 0.7049 (t0) REVERT: A 81 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7297 (ttp) REVERT: D 1 GLU cc_start: 0.7169 (tt0) cc_final: 0.6867 (mm-30) REVERT: D 11 LEU cc_start: 0.8552 (tp) cc_final: 0.8050 (mp) REVERT: D 50 ASP cc_start: 0.8935 (m-30) cc_final: 0.8223 (p0) REVERT: D 93 ASN cc_start: 0.8666 (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: 0.8866 (mp0) cc_final: 0.8589 (mp0) REVERT: C 13 GLU cc_start: 0.8485 (mp0) cc_final: 0.7978 (pm20) REVERT: C 29 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6265 (m-10) REVERT: C 65 GLN cc_start: 0.7953 (tt0) cc_final: 0.7361 (mm110) REVERT: I 11 LEU cc_start: 0.9015 (tp) cc_final: 0.8682 (tt) REVERT: I 13 LEU cc_start: 0.8798 (mt) cc_final: 0.8318 (tm) REVERT: I 93 ASN cc_start: 0.8561 (m-40) cc_final: 0.8158 (t0) REVERT: I 106 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7729 (tm-30) outliers start: 40 outliers final: 15 residues processed: 206 average time/residue: 1.4048 time to fit residues: 322.8318 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 : 2.211 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067079 restraints weight = 37224.653| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.23 r_work: 0.2924 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19193 Z= 0.156 Angle : 0.736 14.547 26237 Z= 0.359 Chirality : 0.048 0.245 3096 Planarity : 0.004 0.039 3206 Dihedral : 10.192 65.883 4306 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 1.90 % Allowed : 12.15 % Favored : 85.95 % 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: -0.48 (0.17), residues: 2252 helix: -0.49 (0.94), residues: 24 sheet: 0.30 (0.16), residues: 961 loop : -0.79 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 178 HIS 0.004 0.001 HIS C 3 PHE 0.015 0.002 PHE L 354 TYR 0.019 0.001 TYR G 121 ARG 0.008 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 24) link_NAG-ASN : angle 2.72172 ( 72) link_ALPHA1-6 : bond 0.00810 ( 12) link_ALPHA1-6 : angle 1.41476 ( 36) link_BETA1-4 : bond 0.00653 ( 40) link_BETA1-4 : angle 2.53312 ( 120) link_ALPHA1-2 : bond 0.00614 ( 4) link_ALPHA1-2 : angle 2.07739 ( 12) link_ALPHA1-3 : bond 0.00918 ( 8) link_ALPHA1-3 : angle 1.71860 ( 24) hydrogen bonds : bond 0.03948 ( 553) hydrogen bonds : angle 6.37750 ( 1497) link_BETA1-6 : bond 0.01395 ( 4) link_BETA1-6 : angle 1.34105 ( 12) SS BOND : bond 0.00767 ( 42) SS BOND : angle 1.52645 ( 84) covalent geometry : bond 0.00349 (19059) covalent geometry : angle 0.69478 (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 203 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 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: symmetry clash REVERT: E 80 TYR cc_start: 0.8626 (m-80) cc_final: 0.8416 (m-10) REVERT: E 86 LEU cc_start: 0.7803 (mt) cc_final: 0.7450 (mp) REVERT: F 82 ASP cc_start: 0.7703 (m-30) cc_final: 0.7488 (m-30) REVERT: F 93 ASN cc_start: 0.8809 (m-40) cc_final: 0.8218 (t0) REVERT: F 109 ARG cc_start: 0.8584 (ptm160) cc_final: 0.6744 (pmt170) REVERT: J 362 MET cc_start: 0.8385 (ptp) cc_final: 0.7995 (ptt) REVERT: A 10 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7588 (mp0) REVERT: A 57 THR cc_start: 0.7849 (m) cc_final: 0.7424 (t) REVERT: A 73 ASP cc_start: 0.7435 (t0) cc_final: 0.7198 (t0) REVERT: A 81 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7328 (ttp) REVERT: A 107 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8782 (m-30) REVERT: D 1 GLU cc_start: 0.7042 (tt0) cc_final: 0.6838 (mm-30) REVERT: D 3 VAL cc_start: 0.9217 (t) cc_final: 0.8899 (m) REVERT: D 11 LEU cc_start: 0.8658 (tp) cc_final: 0.7983 (mp) REVERT: D 50 ASP cc_start: 0.8853 (m-30) cc_final: 0.8199 (p0) REVERT: D 93 ASN cc_start: 0.8660 (m-40) cc_final: 0.8240 (t0) REVERT: D 104 LYS cc_start: 0.9215 (tttt) cc_final: 0.8918 (tmtm) REVERT: K 119 GLU cc_start: 0.8738 (mp0) cc_final: 0.8353 (mp0) REVERT: C 13 GLU cc_start: 0.8526 (mp0) cc_final: 0.8014 (pm20) REVERT: C 46 GLU cc_start: 0.7590 (tt0) cc_final: 0.7344 (tt0) REVERT: C 65 GLN cc_start: 0.7844 (tt0) cc_final: 0.7405 (mm-40) REVERT: C 73 ASP cc_start: 0.6384 (t0) cc_final: 0.6043 (t0) REVERT: C 120 GLN cc_start: 0.7653 (pm20) cc_final: 0.7162 (pm20) REVERT: I 4 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7462 (mmm) REVERT: I 11 LEU cc_start: 0.9043 (tp) cc_final: 0.8488 (tt) REVERT: I 13 LEU cc_start: 0.8795 (mt) cc_final: 0.8342 (tm) REVERT: I 35 TRP cc_start: 0.7846 (m100) cc_final: 0.6653 (m100) REVERT: I 93 ASN cc_start: 0.8616 (m-40) cc_final: 0.8175 (t0) outliers start: 37 outliers final: 15 residues processed: 195 average time/residue: 1.3198 time to fit residues: 288.2497 Evaluate side-chains 162 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 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 81 MET 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: 6.9990 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067194 restraints weight = 37251.580| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.14 r_work: 0.2922 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19193 Z= 0.151 Angle : 0.693 8.669 26237 Z= 0.340 Chirality : 0.047 0.191 3096 Planarity : 0.004 0.041 3206 Dihedral : 7.805 58.141 4306 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 2.47 % Allowed : 12.87 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (1.01), residues: 24 sheet: 0.41 (0.17), residues: 947 loop : -0.79 (0.16), residues: 1281 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 0.015 0.002 PHE J 354 TYR 0.016 0.001 TYR G 121 ARG 0.008 0.000 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 24) link_NAG-ASN : angle 2.50561 ( 72) link_ALPHA1-6 : bond 0.00817 ( 12) link_ALPHA1-6 : angle 1.57938 ( 36) link_BETA1-4 : bond 0.00544 ( 40) link_BETA1-4 : angle 2.31941 ( 120) link_ALPHA1-2 : bond 0.00592 ( 4) link_ALPHA1-2 : angle 2.15223 ( 12) link_ALPHA1-3 : bond 0.00913 ( 8) link_ALPHA1-3 : angle 1.83740 ( 24) hydrogen bonds : bond 0.03699 ( 553) hydrogen bonds : angle 6.22368 ( 1497) link_BETA1-6 : bond 0.01283 ( 4) link_BETA1-6 : angle 1.23555 ( 12) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.24214 ( 84) covalent geometry : bond 0.00345 (19059) covalent geometry : angle 0.65525 (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 209 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.977 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: 0.8623 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: E 80 TYR cc_start: 0.8701 (m-80) cc_final: 0.8445 (m-10) REVERT: E 81 MET cc_start: 0.7757 (tmm) cc_final: 0.7457 (ppp) REVERT: E 86 LEU cc_start: 0.7858 (mt) cc_final: 0.7523 (mp) REVERT: F 82 ASP cc_start: 0.7638 (m-30) cc_final: 0.7373 (m-30) REVERT: F 93 ASN cc_start: 0.8926 (m-40) cc_final: 0.8267 (t0) REVERT: F 109 ARG cc_start: 0.8685 (ptm160) cc_final: 0.6697 (pmt170) REVERT: J 362 MET cc_start: 0.8522 (ptp) cc_final: 0.8206 (ptt) REVERT: A 23 LYS cc_start: 0.8625 (tptp) cc_final: 0.8294 (tppp) REVERT: A 73 ASP cc_start: 0.7510 (t0) cc_final: 0.7178 (OUTLIER) REVERT: A 107 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8883 (m-30) REVERT: D 1 GLU cc_start: 0.7250 (tt0) cc_final: 0.6940 (mm-30) REVERT: D 3 VAL cc_start: 0.9290 (t) cc_final: 0.8973 (m) REVERT: D 4 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (tpt) REVERT: D 11 LEU cc_start: 0.8641 (tp) cc_final: 0.8245 (mm) REVERT: D 93 ASN cc_start: 0.8812 (m-40) cc_final: 0.8281 (t0) REVERT: D 104 LYS cc_start: 0.9204 (tttt) cc_final: 0.8929 (tmtm) REVERT: K 119 GLU cc_start: 0.8868 (mp0) cc_final: 0.8482 (mp0) REVERT: K 128 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8212 (ptmm) REVERT: K 261 LYS cc_start: 0.6597 (tptt) cc_final: 0.6360 (tttt) REVERT: C 13 GLU cc_start: 0.8621 (mp0) cc_final: 0.8070 (pm20) REVERT: C 29 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: C 46 GLU cc_start: 0.7803 (tt0) cc_final: 0.7435 (tt0) REVERT: C 65 GLN cc_start: 0.7799 (tt0) cc_final: 0.7345 (mm-40) REVERT: C 102 ASP cc_start: 0.8998 (p0) cc_final: 0.8710 (p0) REVERT: I 13 LEU cc_start: 0.8793 (mt) cc_final: 0.8304 (tm) REVERT: I 24 ARG cc_start: 0.6648 (tmm-80) cc_final: 0.6294 (tmm-80) REVERT: I 35 TRP cc_start: 0.7958 (m100) cc_final: 0.6715 (m100) REVERT: I 93 ASN cc_start: 0.8810 (m-40) cc_final: 0.8560 (p0) outliers start: 48 outliers final: 25 residues processed: 198 average time/residue: 1.3296 time to fit residues: 295.6934 Evaluate side-chains 177 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 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 75 SER 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 72 THR 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 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 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 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: 3.9990 chunk 213 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** A 62 GLN D 6 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 = 0.3616 r_free = 0.3616 target = 0.095092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065841 restraints weight = 37783.032| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.24 r_work: 0.2900 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19193 Z= 0.187 Angle : 0.718 12.839 26237 Z= 0.355 Chirality : 0.047 0.236 3096 Planarity : 0.004 0.042 3206 Dihedral : 7.483 57.048 4306 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 2.68 % Allowed : 12.61 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.17), residues: 2252 helix: -0.64 (1.00), residues: 24 sheet: 0.31 (0.17), residues: 955 loop : -0.86 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 178 HIS 0.004 0.001 HIS G 144 PHE 0.016 0.002 PHE J 354 TYR 0.018 0.002 TYR G 121 ARG 0.008 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 24) link_NAG-ASN : angle 2.60439 ( 72) link_ALPHA1-6 : bond 0.00705 ( 12) link_ALPHA1-6 : angle 1.41567 ( 36) link_BETA1-4 : bond 0.00529 ( 40) link_BETA1-4 : angle 2.12572 ( 120) link_ALPHA1-2 : bond 0.00514 ( 4) link_ALPHA1-2 : angle 2.23234 ( 12) link_ALPHA1-3 : bond 0.00804 ( 8) link_ALPHA1-3 : angle 1.97660 ( 24) hydrogen bonds : bond 0.03900 ( 553) hydrogen bonds : angle 6.25075 ( 1497) link_BETA1-6 : bond 0.01221 ( 4) link_BETA1-6 : angle 1.23884 ( 12) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.40814 ( 84) covalent geometry : bond 0.00440 (19059) covalent geometry : angle 0.68363 (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 205 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 1.976 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: 0.8660 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: E 80 TYR cc_start: 0.8742 (m-80) cc_final: 0.8540 (m-10) REVERT: E 81 MET cc_start: 0.7719 (tmm) cc_final: 0.7407 (ppp) REVERT: E 86 LEU cc_start: 0.7872 (mt) cc_final: 0.7456 (mp) REVERT: F 17 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: F 79 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7435 (mm110) REVERT: F 82 ASP cc_start: 0.7513 (m-30) cc_final: 0.7240 (m-30) REVERT: F 93 ASN cc_start: 0.8971 (m-40) cc_final: 0.8267 (t0) REVERT: F 109 ARG cc_start: 0.8524 (ptm160) cc_final: 0.6403 (ptp-170) REVERT: J 128 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7777 (ptmt) REVERT: A 23 LYS cc_start: 0.8593 (tptp) cc_final: 0.8291 (tppp) REVERT: A 81 MET cc_start: 0.7757 (tmm) cc_final: 0.7427 (ttt) REVERT: A 102 ASP cc_start: 0.9082 (p0) cc_final: 0.8871 (p0) REVERT: A 107 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8933 (m-30) REVERT: D 1 GLU cc_start: 0.7249 (tt0) cc_final: 0.6918 (mm-30) REVERT: D 3 VAL cc_start: 0.9296 (t) cc_final: 0.8979 (m) REVERT: D 11 LEU cc_start: 0.8623 (tp) cc_final: 0.8213 (mm) REVERT: D 93 ASN cc_start: 0.8859 (m-40) cc_final: 0.8249 (t0) REVERT: D 104 LYS cc_start: 0.9232 (tttt) cc_final: 0.8877 (tmtm) REVERT: K 119 GLU cc_start: 0.8900 (mp0) cc_final: 0.8523 (mp0) REVERT: K 128 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8024 (ptmm) REVERT: K 261 LYS cc_start: 0.6657 (tptt) cc_final: 0.6425 (tttm) REVERT: C 10 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: C 13 GLU cc_start: 0.8618 (mp0) cc_final: 0.8056 (pm20) REVERT: C 46 GLU cc_start: 0.7864 (tt0) cc_final: 0.7486 (tt0) REVERT: C 65 GLN cc_start: 0.7882 (tt0) cc_final: 0.7374 (mm-40) REVERT: C 73 ASP cc_start: 0.6715 (t0) cc_final: 0.6278 (t0) REVERT: C 102 ASP cc_start: 0.9025 (p0) cc_final: 0.8757 (p0) REVERT: I 4 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: I 13 LEU cc_start: 0.8899 (mt) cc_final: 0.8389 (tm) REVERT: I 24 ARG cc_start: 0.6664 (tmm-80) cc_final: 0.6293 (tmm-80) REVERT: I 35 TRP cc_start: 0.7980 (m100) cc_final: 0.6701 (m100) REVERT: I 93 ASN cc_start: 0.8872 (m-40) cc_final: 0.8657 (p0) outliers start: 52 outliers final: 26 residues processed: 191 average time/residue: 1.3658 time to fit residues: 291.6657 Evaluate side-chains 178 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 28 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068232 restraints weight = 37132.191| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.15 r_work: 0.2955 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19193 Z= 0.114 Angle : 0.655 12.094 26237 Z= 0.324 Chirality : 0.045 0.185 3096 Planarity : 0.003 0.042 3206 Dihedral : 6.749 49.291 4306 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 1.90 % Allowed : 13.28 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.17), residues: 2252 helix: -0.76 (1.02), residues: 24 sheet: 0.39 (0.17), residues: 959 loop : -0.73 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.003 0.000 HIS C 3 PHE 0.012 0.001 PHE C 29 TYR 0.014 0.001 TYR F 49 ARG 0.009 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 24) link_NAG-ASN : angle 2.17897 ( 72) link_ALPHA1-6 : bond 0.00781 ( 12) link_ALPHA1-6 : angle 1.32241 ( 36) link_BETA1-4 : bond 0.00551 ( 40) link_BETA1-4 : angle 1.76139 ( 120) link_ALPHA1-2 : bond 0.00685 ( 4) link_ALPHA1-2 : angle 2.16681 ( 12) link_ALPHA1-3 : bond 0.01069 ( 8) link_ALPHA1-3 : angle 1.56401 ( 24) hydrogen bonds : bond 0.03272 ( 553) hydrogen bonds : angle 5.99474 ( 1497) link_BETA1-6 : bond 0.01122 ( 4) link_BETA1-6 : angle 1.27078 ( 12) SS BOND : bond 0.00477 ( 42) SS BOND : angle 1.19609 ( 84) covalent geometry : bond 0.00249 (19059) covalent geometry : angle 0.62874 (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 202 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.946 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: 0.8535 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: E 80 TYR cc_start: 0.8733 (m-80) cc_final: 0.8509 (m-10) REVERT: E 81 MET cc_start: 0.7704 (tmm) cc_final: 0.7392 (ppp) REVERT: E 86 LEU cc_start: 0.7952 (mt) cc_final: 0.7592 (mp) REVERT: F 61 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7265 (mtm110) REVERT: F 93 ASN cc_start: 0.8812 (m-40) cc_final: 0.8104 (t0) REVERT: F 109 ARG cc_start: 0.8541 (ptm160) cc_final: 0.6477 (ptp-170) REVERT: A 81 MET cc_start: 0.7780 (tmm) cc_final: 0.7466 (ttt) REVERT: A 102 ASP cc_start: 0.8977 (p0) cc_final: 0.8733 (p0) REVERT: D 1 GLU cc_start: 0.7188 (tt0) cc_final: 0.6880 (mm-30) REVERT: D 3 VAL cc_start: 0.9380 (t) cc_final: 0.9106 (m) REVERT: D 11 LEU cc_start: 0.8609 (tp) cc_final: 0.8217 (mm) REVERT: D 93 ASN cc_start: 0.8695 (m-40) cc_final: 0.7957 (t0) REVERT: D 104 LYS cc_start: 0.9216 (tttt) cc_final: 0.8890 (tmtm) REVERT: D 106 GLU cc_start: 0.8589 (tp30) cc_final: 0.8369 (tp30) REVERT: K 119 GLU cc_start: 0.8669 (mp0) cc_final: 0.8209 (mp0) REVERT: C 10 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: C 13 GLU cc_start: 0.8585 (mp0) cc_final: 0.8042 (pm20) REVERT: C 46 GLU cc_start: 0.7742 (tt0) cc_final: 0.7391 (tt0) REVERT: C 65 GLN cc_start: 0.7746 (tt0) cc_final: 0.7225 (mm-40) REVERT: C 102 ASP cc_start: 0.8912 (p0) cc_final: 0.8598 (p0) REVERT: I 4 MET cc_start: 0.8081 (mmm) cc_final: 0.7407 (mmm) REVERT: I 13 LEU cc_start: 0.9026 (mt) cc_final: 0.8584 (tm) REVERT: I 24 ARG cc_start: 0.6636 (tmm-80) cc_final: 0.6342 (tmm-80) REVERT: I 35 TRP cc_start: 0.7823 (m100) cc_final: 0.6519 (m100) REVERT: I 75 ILE cc_start: 0.9150 (mt) cc_final: 0.8776 (tp) REVERT: I 88 CYS cc_start: 0.6667 (p) cc_final: 0.6076 (p) outliers start: 37 outliers final: 17 residues processed: 194 average time/residue: 1.3888 time to fit residues: 301.9337 Evaluate side-chains 162 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 110 THR 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 75 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 10 GLU 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: 0.9990 chunk 135 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN K 226 GLN ** L 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 = 0.3617 r_free = 0.3617 target = 0.095195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066765 restraints weight = 37189.081| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.15 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19193 Z= 0.154 Angle : 0.687 12.563 26237 Z= 0.341 Chirality : 0.046 0.193 3096 Planarity : 0.004 0.046 3206 Dihedral : 6.795 49.141 4306 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 2.37 % Allowed : 13.69 % Favored : 83.94 % 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: -0.59 (1.06), residues: 24 sheet: 0.40 (0.17), residues: 927 loop : -0.74 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 178 HIS 0.004 0.001 HIS G 144 PHE 0.015 0.002 PHE J 354 TYR 0.016 0.001 TYR G 121 ARG 0.013 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 24) link_NAG-ASN : angle 2.40270 ( 72) link_ALPHA1-6 : bond 0.00692 ( 12) link_ALPHA1-6 : angle 1.39552 ( 36) link_BETA1-4 : bond 0.00494 ( 40) link_BETA1-4 : angle 1.77913 ( 120) link_ALPHA1-2 : bond 0.00529 ( 4) link_ALPHA1-2 : angle 2.17069 ( 12) link_ALPHA1-3 : bond 0.00902 ( 8) link_ALPHA1-3 : angle 1.85148 ( 24) hydrogen bonds : bond 0.03578 ( 553) hydrogen bonds : angle 6.00624 ( 1497) link_BETA1-6 : bond 0.01066 ( 4) link_BETA1-6 : angle 1.22109 ( 12) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.22194 ( 84) covalent geometry : bond 0.00360 (19059) covalent geometry : angle 0.65916 (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 194 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 1.995 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: 0.8638 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: G 431 LYS cc_start: 0.8181 (tptp) cc_final: 0.7961 (tppt) REVERT: E 43 GLN cc_start: 0.7691 (mm110) cc_final: 0.7460 (mp10) REVERT: E 63 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.8171 (ptp90) REVERT: E 80 TYR cc_start: 0.8773 (m-80) cc_final: 0.8550 (m-10) REVERT: E 81 MET cc_start: 0.7755 (tmm) cc_final: 0.7440 (ppp) REVERT: E 86 LEU cc_start: 0.7947 (mt) cc_final: 0.7548 (mp) REVERT: F 24 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.7928 (ttp-110) REVERT: F 61 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7549 (mtm110) REVERT: F 82 ASP cc_start: 0.7721 (m-30) cc_final: 0.7495 (m-30) REVERT: F 93 ASN cc_start: 0.8961 (m-40) cc_final: 0.8239 (t0) REVERT: F 109 ARG cc_start: 0.8514 (ptm160) cc_final: 0.6575 (ptp-170) REVERT: A 10 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6925 (mm-30) REVERT: A 23 LYS cc_start: 0.8485 (tptp) cc_final: 0.8235 (tppp) REVERT: A 73 ASP cc_start: 0.8282 (t0) cc_final: 0.7342 (p0) REVERT: A 81 MET cc_start: 0.7805 (tmm) cc_final: 0.6980 (ttp) REVERT: A 102 ASP cc_start: 0.8969 (p0) cc_final: 0.8712 (p0) REVERT: D 1 GLU cc_start: 0.7353 (tt0) cc_final: 0.6972 (mm-30) REVERT: D 3 VAL cc_start: 0.9380 (t) cc_final: 0.9064 (m) REVERT: D 11 LEU cc_start: 0.8655 (tp) cc_final: 0.8200 (mm) REVERT: D 24 ARG cc_start: 0.7471 (ptm-80) cc_final: 0.7093 (ppp80) REVERT: D 93 ASN cc_start: 0.8857 (m-40) cc_final: 0.8117 (t0) REVERT: D 104 LYS cc_start: 0.9211 (tttt) cc_final: 0.8867 (tmtm) REVERT: D 106 GLU cc_start: 0.8639 (tp30) cc_final: 0.8437 (tp30) REVERT: D 109 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7400 (pmt170) REVERT: K 119 GLU cc_start: 0.8859 (mp0) cc_final: 0.8447 (mp0) REVERT: K 150 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7992 (mtm110) REVERT: L 113 ASP cc_start: 0.7727 (p0) cc_final: 0.7522 (p0) REVERT: C 10 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: C 13 GLU cc_start: 0.8599 (mp0) cc_final: 0.8052 (pm20) REVERT: C 46 GLU cc_start: 0.7957 (tt0) cc_final: 0.7659 (tt0) REVERT: C 65 GLN cc_start: 0.7829 (tt0) cc_final: 0.7350 (mm-40) REVERT: C 73 ASP cc_start: 0.7015 (t0) cc_final: 0.6603 (t0) REVERT: C 102 ASP cc_start: 0.9020 (p0) cc_final: 0.8729 (p0) REVERT: I 13 LEU cc_start: 0.9028 (mt) cc_final: 0.8581 (tm) REVERT: I 24 ARG cc_start: 0.6679 (tmm-80) cc_final: 0.6252 (tmm160) REVERT: I 35 TRP cc_start: 0.8007 (m100) cc_final: 0.6730 (m100) REVERT: I 75 ILE cc_start: 0.9136 (mt) cc_final: 0.8759 (tp) REVERT: I 88 CYS cc_start: 0.7257 (p) cc_final: 0.6557 (p) outliers start: 46 outliers final: 20 residues processed: 187 average time/residue: 1.4267 time to fit residues: 297.3688 Evaluate side-chains 164 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 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 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain C residue 10 GLU 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: 0.9980 chunk 184 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065531 restraints weight = 37468.887| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.14 r_work: 0.2924 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19193 Z= 0.186 Angle : 0.713 12.667 26237 Z= 0.354 Chirality : 0.047 0.193 3096 Planarity : 0.004 0.045 3206 Dihedral : 7.000 50.821 4306 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 1.80 % Allowed : 14.77 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.17), residues: 2252 helix: -0.59 (1.05), residues: 24 sheet: 0.34 (0.17), residues: 931 loop : -0.89 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 178 HIS 0.005 0.001 HIS G 144 PHE 0.016 0.002 PHE J 422 TYR 0.017 0.002 TYR G 121 ARG 0.012 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 24) link_NAG-ASN : angle 2.45045 ( 72) link_ALPHA1-6 : bond 0.00677 ( 12) link_ALPHA1-6 : angle 1.38691 ( 36) link_BETA1-4 : bond 0.00483 ( 40) link_BETA1-4 : angle 1.74707 ( 120) link_ALPHA1-2 : bond 0.00459 ( 4) link_ALPHA1-2 : angle 2.32476 ( 12) link_ALPHA1-3 : bond 0.00790 ( 8) link_ALPHA1-3 : angle 2.02339 ( 24) hydrogen bonds : bond 0.03836 ( 553) hydrogen bonds : angle 6.04735 ( 1497) link_BETA1-6 : bond 0.01066 ( 4) link_BETA1-6 : angle 1.23203 ( 12) SS BOND : bond 0.00469 ( 42) SS BOND : angle 1.24529 ( 84) covalent geometry : bond 0.00441 (19059) covalent geometry : angle 0.68550 (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: 35 poor density : 147 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.8413 (tt0) cc_final: 0.8213 (tt0) REVERT: E 80 TYR cc_start: 0.8846 (m-80) cc_final: 0.8640 (m-10) REVERT: E 81 MET cc_start: 0.7968 (tmm) cc_final: 0.7658 (ppp) REVERT: E 86 LEU cc_start: 0.8130 (mt) cc_final: 0.7717 (mp) REVERT: F 18 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.8349 (tmm-80) REVERT: F 24 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8332 (ttp-110) REVERT: F 61 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7512 (mtm110) REVERT: F 93 ASN cc_start: 0.8940 (m-40) cc_final: 0.8290 (t0) REVERT: F 109 ARG cc_start: 0.8502 (ptm160) cc_final: 0.6599 (ptp-170) REVERT: J 362 MET cc_start: 0.8543 (ptp) cc_final: 0.8235 (ptt) REVERT: A 10 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 73 ASP cc_start: 0.8244 (t0) cc_final: 0.7419 (p0) REVERT: A 80 TYR cc_start: 0.8523 (m-10) cc_final: 0.7855 (m-10) REVERT: A 81 MET cc_start: 0.8037 (tmm) cc_final: 0.7686 (ttt) REVERT: A 102 ASP cc_start: 0.9018 (p0) cc_final: 0.8753 (p0) REVERT: D 1 GLU cc_start: 0.7232 (tt0) cc_final: 0.6962 (mm-30) REVERT: D 3 VAL cc_start: 0.9386 (t) cc_final: 0.9081 (m) REVERT: D 4 MET cc_start: 0.7821 (mtp) cc_final: 0.7601 (mtp) REVERT: D 11 LEU cc_start: 0.8754 (tp) cc_final: 0.8272 (mm) REVERT: D 24 ARG cc_start: 0.7772 (ptm-80) cc_final: 0.7426 (ppp80) REVERT: D 37 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: D 81 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8173 (tp30) REVERT: D 93 ASN cc_start: 0.8851 (m-40) cc_final: 0.8215 (t0) REVERT: D 104 LYS cc_start: 0.9226 (tttt) cc_final: 0.8902 (tmtm) REVERT: D 106 GLU cc_start: 0.8641 (tp30) cc_final: 0.8441 (tp30) REVERT: D 109 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7418 (pmt170) REVERT: K 119 GLU cc_start: 0.8869 (mp0) cc_final: 0.8569 (mp0) REVERT: C 10 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: C 13 GLU cc_start: 0.8645 (mp0) cc_final: 0.8068 (pm20) REVERT: C 46 GLU cc_start: 0.8261 (tt0) cc_final: 0.7942 (tt0) REVERT: C 65 GLN cc_start: 0.8018 (tt0) cc_final: 0.7687 (mm-40) REVERT: C 74 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7887 (pm20) REVERT: C 102 ASP cc_start: 0.9154 (p0) cc_final: 0.8850 (p0) REVERT: I 13 LEU cc_start: 0.9063 (mt) cc_final: 0.8649 (tm) REVERT: I 24 ARG cc_start: 0.6659 (tmm-80) cc_final: 0.6296 (tmm160) REVERT: I 35 TRP cc_start: 0.8218 (m100) cc_final: 0.7010 (m100) REVERT: I 75 ILE cc_start: 0.9219 (mt) cc_final: 0.8832 (tp) REVERT: I 88 CYS cc_start: 0.7334 (p) cc_final: 0.6803 (p) outliers start: 35 outliers final: 23 residues processed: 178 average time/residue: 1.4596 time to fit residues: 289.3000 Evaluate side-chains 162 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 110 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 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 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 10 GLU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 214 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.0170 chunk 18 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.096355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067286 restraints weight = 37261.820| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.15 r_work: 0.2957 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19193 Z= 0.128 Angle : 0.671 12.145 26237 Z= 0.334 Chirality : 0.045 0.190 3096 Planarity : 0.004 0.051 3206 Dihedral : 6.548 46.586 4306 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 1.75 % Allowed : 15.13 % Favored : 83.12 % 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: -0.46 (0.17), residues: 2252 helix: -0.77 (1.01), residues: 24 sheet: 0.34 (0.17), residues: 943 loop : -0.79 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 PHE 0.014 0.002 PHE G 410 TYR 0.012 0.001 TYR C 95 ARG 0.013 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 24) link_NAG-ASN : angle 2.16250 ( 72) link_ALPHA1-6 : bond 0.00722 ( 12) link_ALPHA1-6 : angle 1.32421 ( 36) link_BETA1-4 : bond 0.00524 ( 40) link_BETA1-4 : angle 1.55197 ( 120) link_ALPHA1-2 : bond 0.00590 ( 4) link_ALPHA1-2 : angle 2.25211 ( 12) link_ALPHA1-3 : bond 0.00978 ( 8) link_ALPHA1-3 : angle 1.65316 ( 24) hydrogen bonds : bond 0.03358 ( 553) hydrogen bonds : angle 5.90873 ( 1497) link_BETA1-6 : bond 0.01011 ( 4) link_BETA1-6 : angle 1.27123 ( 12) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.07988 ( 84) covalent geometry : bond 0.00295 (19059) covalent geometry : angle 0.64877 (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 183 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.989 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: 0.8237 (p-80) cc_final: 0.7720 (m-70) REVERT: E 23 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8312 (mtpp) REVERT: E 63 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.8049 (ptp90) REVERT: E 80 TYR cc_start: 0.8847 (m-80) cc_final: 0.8639 (m-10) REVERT: E 81 MET cc_start: 0.7932 (tmm) cc_final: 0.7631 (ppp) REVERT: E 86 LEU cc_start: 0.8117 (mt) cc_final: 0.7757 (mp) REVERT: E 107 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: F 24 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8345 (ttp-110) REVERT: F 93 ASN cc_start: 0.8908 (m-40) cc_final: 0.8277 (t0) REVERT: F 109 ARG cc_start: 0.8496 (ptm160) cc_final: 0.6636 (ptp-170) REVERT: A 10 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 23 LYS cc_start: 0.8563 (tptp) cc_final: 0.8339 (tppp) REVERT: A 73 ASP cc_start: 0.8276 (t0) cc_final: 0.7444 (p0) REVERT: A 81 MET cc_start: 0.8004 (tmm) cc_final: 0.7646 (ttt) REVERT: A 102 ASP cc_start: 0.8996 (p0) cc_final: 0.8736 (p0) REVERT: D 1 GLU cc_start: 0.7229 (tt0) cc_final: 0.6946 (mm-30) REVERT: D 3 VAL cc_start: 0.9400 (t) cc_final: 0.9105 (m) REVERT: D 11 LEU cc_start: 0.8717 (tp) cc_final: 0.8250 (mm) REVERT: D 24 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7206 (ppp80) REVERT: D 37 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: D 93 ASN cc_start: 0.8815 (m-40) cc_final: 0.8157 (t0) REVERT: D 104 LYS cc_start: 0.9193 (tttt) cc_final: 0.8872 (tmtm) REVERT: D 109 ARG cc_start: 0.7797 (ptm160) cc_final: 0.7413 (pmt170) REVERT: K 119 GLU cc_start: 0.8828 (mp0) cc_final: 0.8482 (mp0) REVERT: C 10 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: C 13 GLU cc_start: 0.8591 (mp0) cc_final: 0.8043 (pm20) REVERT: C 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7869 (tt0) REVERT: C 65 GLN cc_start: 0.7887 (tt0) cc_final: 0.7579 (mm-40) REVERT: C 102 ASP cc_start: 0.9139 (p0) cc_final: 0.8844 (p0) REVERT: C 111 GLU cc_start: 0.7931 (tp30) cc_final: 0.7461 (tp30) REVERT: I 13 LEU cc_start: 0.9092 (mt) cc_final: 0.8615 (tp) REVERT: I 24 ARG cc_start: 0.6738 (tmm-80) cc_final: 0.6372 (tmm160) REVERT: I 35 TRP cc_start: 0.8203 (m100) cc_final: 0.6928 (m100) REVERT: I 75 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8568 (tp) REVERT: I 88 CYS cc_start: 0.7410 (p) cc_final: 0.6797 (p) outliers start: 34 outliers final: 14 residues processed: 176 average time/residue: 1.4446 time to fit residues: 284.8053 Evaluate side-chains 161 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 10 GLU 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: 0.8980 chunk 7 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.095556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067039 restraints weight = 37131.595| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.07 r_work: 0.2955 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19193 Z= 0.143 Angle : 0.690 12.286 26237 Z= 0.344 Chirality : 0.046 0.194 3096 Planarity : 0.004 0.051 3206 Dihedral : 6.526 45.650 4306 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 1.39 % Allowed : 15.80 % Favored : 82.81 % 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: -0.51 (0.17), residues: 2252 helix: -0.74 (1.02), residues: 24 sheet: 0.35 (0.17), residues: 919 loop : -0.83 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 178 HIS 0.003 0.001 HIS G 184 PHE 0.015 0.002 PHE G 410 TYR 0.018 0.001 TYR F 49 ARG 0.013 0.001 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 24) link_NAG-ASN : angle 2.20548 ( 72) link_ALPHA1-6 : bond 0.00687 ( 12) link_ALPHA1-6 : angle 1.36889 ( 36) link_BETA1-4 : bond 0.00498 ( 40) link_BETA1-4 : angle 1.57793 ( 120) link_ALPHA1-2 : bond 0.00550 ( 4) link_ALPHA1-2 : angle 2.24735 ( 12) link_ALPHA1-3 : bond 0.00912 ( 8) link_ALPHA1-3 : angle 1.75056 ( 24) hydrogen bonds : bond 0.03472 ( 553) hydrogen bonds : angle 5.90650 ( 1497) link_BETA1-6 : bond 0.00992 ( 4) link_BETA1-6 : angle 1.24522 ( 12) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.27686 ( 84) covalent geometry : bond 0.00335 (19059) covalent geometry : angle 0.66610 (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 165 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8323 (mtpp) REVERT: E 80 TYR cc_start: 0.8852 (m-80) cc_final: 0.8652 (m-10) REVERT: E 81 MET cc_start: 0.7973 (tmm) cc_final: 0.7672 (ppp) REVERT: E 86 LEU cc_start: 0.8144 (mt) cc_final: 0.7749 (mp) REVERT: E 107 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: F 24 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8342 (ttp-110) REVERT: F 61 ARG cc_start: 0.7614 (mtm110) cc_final: 0.6903 (ttp-170) REVERT: F 82 ASP cc_start: 0.7650 (m-30) cc_final: 0.6698 (m-30) REVERT: F 93 ASN cc_start: 0.8910 (m-40) cc_final: 0.8269 (t0) REVERT: F 109 ARG cc_start: 0.8505 (ptm160) cc_final: 0.6654 (ptp-170) REVERT: A 10 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 23 LYS cc_start: 0.8546 (tptp) cc_final: 0.8260 (tppp) REVERT: A 81 MET cc_start: 0.8040 (tmm) cc_final: 0.7667 (ttt) REVERT: A 102 ASP cc_start: 0.8999 (p0) cc_final: 0.8730 (p0) REVERT: D 1 GLU cc_start: 0.7194 (tt0) cc_final: 0.6768 (tm-30) REVERT: D 3 VAL cc_start: 0.9389 (t) cc_final: 0.9105 (m) REVERT: D 11 LEU cc_start: 0.8721 (tp) cc_final: 0.8257 (mm) REVERT: D 24 ARG cc_start: 0.7662 (ptm-80) cc_final: 0.7315 (ppp80) REVERT: D 37 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: D 61 ARG cc_start: 0.8405 (ptm160) cc_final: 0.8198 (ptm160) REVERT: D 81 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7921 (tp30) REVERT: D 93 ASN cc_start: 0.8818 (m-40) cc_final: 0.8158 (t0) REVERT: D 104 LYS cc_start: 0.9201 (tttt) cc_final: 0.8891 (tmtm) REVERT: D 106 GLU cc_start: 0.8476 (tp30) cc_final: 0.8254 (tp30) REVERT: D 109 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7418 (pmt170) REVERT: K 119 GLU cc_start: 0.8838 (mp0) cc_final: 0.8478 (mp0) REVERT: C 10 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: C 13 GLU cc_start: 0.8603 (mp0) cc_final: 0.8069 (pm20) REVERT: C 46 GLU cc_start: 0.8198 (tt0) cc_final: 0.7903 (tt0) REVERT: C 65 GLN cc_start: 0.7904 (tt0) cc_final: 0.7588 (mm-40) REVERT: C 102 ASP cc_start: 0.9139 (p0) cc_final: 0.8846 (p0) REVERT: I 4 MET cc_start: 0.8249 (mmm) cc_final: 0.7124 (tpp) REVERT: I 13 LEU cc_start: 0.9065 (mt) cc_final: 0.8649 (tm) REVERT: I 24 ARG cc_start: 0.6671 (tmm-80) cc_final: 0.6406 (tmm160) REVERT: I 75 ILE cc_start: 0.9112 (mt) cc_final: 0.8827 (tp) outliers start: 27 outliers final: 17 residues processed: 163 average time/residue: 1.4888 time to fit residues: 271.0128 Evaluate side-chains 155 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain L residue 376 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 154 optimal weight: 0.0020 chunk 123 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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** ** 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 = 0.3638 r_free = 0.3638 target = 0.095547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067229 restraints weight = 37102.649| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.05 r_work: 0.2956 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 19193 Z= 0.183 Angle : 0.867 59.186 26237 Z= 0.474 Chirality : 0.045 0.191 3096 Planarity : 0.004 0.054 3206 Dihedral : 6.533 45.627 4306 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 1.34 % Allowed : 16.11 % Favored : 82.55 % Cbeta Deviations : 0.05 % 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: -0.51 (0.17), residues: 2252 helix: -0.75 (1.02), residues: 24 sheet: 0.35 (0.17), residues: 919 loop : -0.84 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 178 HIS 0.003 0.001 HIS C 3 PHE 0.015 0.002 PHE G 410 TYR 0.013 0.001 TYR J 121 ARG 0.020 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 24) link_NAG-ASN : angle 2.20850 ( 72) link_ALPHA1-6 : bond 0.00680 ( 12) link_ALPHA1-6 : angle 1.36911 ( 36) link_BETA1-4 : bond 0.00496 ( 40) link_BETA1-4 : angle 1.57450 ( 120) link_ALPHA1-2 : bond 0.00555 ( 4) link_ALPHA1-2 : angle 2.24106 ( 12) link_ALPHA1-3 : bond 0.01018 ( 8) link_ALPHA1-3 : angle 1.79748 ( 24) hydrogen bonds : bond 0.03446 ( 553) hydrogen bonds : angle 5.90973 ( 1497) link_BETA1-6 : bond 0.00983 ( 4) link_BETA1-6 : angle 1.24733 ( 12) SS BOND : bond 0.00478 ( 42) SS BOND : angle 2.67050 ( 84) covalent geometry : bond 0.00379 (19059) covalent geometry : angle 0.84001 (25877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13397.93 seconds wall clock time: 231 minutes 40.13 seconds (13900.13 seconds total)