Starting phenix.real_space_refine on Tue Nov 19 07:32:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_29704.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_29704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_29704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_29704.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3m_29704/11_2024/8g3m_29704.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11520 2.51 5 N 3120 2.21 5 O 3913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.20, per 1000 atoms: 0.65 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: 6.40 Conformation dependent library (CDL) restraints added in 2.8 seconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 40 sheets defined 4.1% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 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: 6.90 Time building geometry restraints manager: 6.70 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: 2.770 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 45.410 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.030 ------------------------------------------------------------------------------- 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 : 0.016 0.086 19059 Z= 1.059 Angle : 1.788 9.291 25877 Z= 1.163 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 *********************** 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 : 1.996 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: 1.4779 time to fit residues: 467.7654 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 : 2.031 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 19059 Z= 0.212 Angle : 0.739 9.243 25877 Z= 0.379 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 2.024 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 86 LEU cc_start: 0.8275 (mt) cc_final: 0.7850 (mp) REVERT: E 90 ASP cc_start: 0.8381 (m-30) cc_final: 0.8178 (m-30) REVERT: F 1 GLU cc_start: 0.7844 (tt0) cc_final: 0.7336 (tm-30) REVERT: F 17 GLU cc_start: 0.8334 (mp0) cc_final: 0.8000 (mp0) REVERT: F 93 ASN cc_start: 0.9088 (m-40) cc_final: 0.8693 (t0) REVERT: F 109 ARG cc_start: 0.7717 (ptm160) cc_final: 0.5684 (pmt170) REVERT: A 10 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7532 (mp0) REVERT: A 73 ASP cc_start: 0.7804 (t0) cc_final: 0.7531 (t0) REVERT: D 1 GLU cc_start: 0.7999 (tt0) cc_final: 0.7573 (mm-30) REVERT: D 11 LEU cc_start: 0.8309 (tp) cc_final: 0.7879 (mp) REVERT: D 50 ASP cc_start: 0.9178 (m-30) cc_final: 0.8459 (p0) REVERT: D 93 ASN cc_start: 0.9018 (m-40) cc_final: 0.8803 (t0) REVERT: D 104 LYS cc_start: 0.9263 (tttt) cc_final: 0.9060 (tmtm) REVERT: C 13 GLU cc_start: 0.8904 (mp0) cc_final: 0.8507 (pm20) REVERT: C 29 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: C 65 GLN cc_start: 0.8162 (tt0) cc_final: 0.7677 (mm110) REVERT: C 74 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8142 (pm20) REVERT: I 11 LEU cc_start: 0.8835 (tp) cc_final: 0.8539 (tt) REVERT: I 13 LEU cc_start: 0.8643 (mt) cc_final: 0.8220 (tm) REVERT: I 93 ASN cc_start: 0.8886 (m-40) cc_final: 0.8677 (t0) REVERT: I 106 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7987 (tm-30) outliers start: 40 outliers final: 15 residues processed: 206 average time/residue: 1.5265 time to fit residues: 350.3772 Evaluate side-chains 161 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 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 113 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 202 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 19059 Z= 0.432 Angle : 0.795 15.077 25877 Z= 0.403 Chirality : 0.052 0.283 3096 Planarity : 0.005 0.038 3206 Dihedral : 10.734 70.197 4306 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 2.42 % Allowed : 11.99 % Favored : 85.59 % 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: -0.88 (0.16), residues: 2252 helix: -0.63 (0.89), residues: 24 sheet: 0.12 (0.17), residues: 950 loop : -1.15 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 178 HIS 0.007 0.002 HIS G 144 PHE 0.020 0.003 PHE J 422 TYR 0.025 0.002 TYR G 121 ARG 0.008 0.001 ARG F 45 *********************** 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 206 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 LEU cc_start: 0.8444 (mt) cc_final: 0.8016 (mp) REVERT: F 1 GLU cc_start: 0.8027 (tt0) cc_final: 0.7747 (tp30) REVERT: F 93 ASN cc_start: 0.9172 (m-40) cc_final: 0.8766 (t0) REVERT: F 109 ARG cc_start: 0.8174 (ptm160) cc_final: 0.6496 (pmt170) REVERT: A 57 THR cc_start: 0.8474 (m) cc_final: 0.8202 (t) REVERT: A 107 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8956 (m-30) REVERT: D 1 GLU cc_start: 0.8115 (tt0) cc_final: 0.7716 (mm-30) REVERT: D 11 LEU cc_start: 0.8407 (tp) cc_final: 0.8017 (mm) REVERT: D 50 ASP cc_start: 0.9183 (m-30) cc_final: 0.8495 (p0) REVERT: D 93 ASN cc_start: 0.9188 (m-40) cc_final: 0.8843 (t0) REVERT: D 104 LYS cc_start: 0.9260 (tttt) cc_final: 0.9029 (tmtm) REVERT: K 261 LYS cc_start: 0.7260 (tptt) cc_final: 0.7044 (tttt) REVERT: C 10 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7641 (tm-30) REVERT: C 13 GLU cc_start: 0.8975 (mp0) cc_final: 0.8582 (pm20) REVERT: C 29 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: C 65 GLN cc_start: 0.8417 (tt0) cc_final: 0.8050 (mm-40) REVERT: C 74 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8129 (pm20) REVERT: I 4 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: I 11 LEU cc_start: 0.8891 (tp) cc_final: 0.8385 (tt) REVERT: I 13 LEU cc_start: 0.8637 (mt) cc_final: 0.8256 (tm) REVERT: I 24 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.7143 (tmm-80) REVERT: I 35 TRP cc_start: 0.8407 (m100) cc_final: 0.7507 (m100) REVERT: I 93 ASN cc_start: 0.9068 (m-40) cc_final: 0.8703 (t0) outliers start: 47 outliers final: 19 residues processed: 198 average time/residue: 1.4568 time to fit residues: 322.8138 Evaluate side-chains 162 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 29 PHE 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 201 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN A 62 GLN K 441 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19059 Z= 0.190 Angle : 0.662 9.519 25877 Z= 0.333 Chirality : 0.047 0.201 3096 Planarity : 0.004 0.040 3206 Dihedral : 8.111 59.295 4306 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 2.16 % Allowed : 13.33 % Favored : 84.51 % 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: -0.64 (0.17), residues: 2252 helix: -0.54 (1.02), residues: 24 sheet: 0.27 (0.17), residues: 957 loop : -0.98 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 178 HIS 0.003 0.001 HIS C 3 PHE 0.013 0.002 PHE K 410 TYR 0.013 0.001 TYR G 121 ARG 0.006 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 467 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7667 (ptm) REVERT: E 81 MET cc_start: 0.8214 (tmm) cc_final: 0.7916 (ppp) REVERT: E 86 LEU cc_start: 0.8458 (mt) cc_final: 0.8052 (mp) REVERT: F 1 GLU cc_start: 0.7975 (tt0) cc_final: 0.7707 (tp30) REVERT: F 82 ASP cc_start: 0.7612 (m-30) cc_final: 0.7406 (m-30) REVERT: F 93 ASN cc_start: 0.9134 (m-40) cc_final: 0.8704 (t0) REVERT: F 109 ARG cc_start: 0.8125 (ptm160) cc_final: 0.6428 (pmt170) REVERT: A 10 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7619 (mp0) REVERT: A 81 MET cc_start: 0.7669 (ttp) cc_final: 0.7165 (ttp) REVERT: D 1 GLU cc_start: 0.8066 (tt0) cc_final: 0.7641 (mm-30) REVERT: D 3 VAL cc_start: 0.9359 (t) cc_final: 0.9134 (m) REVERT: D 4 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8238 (tpt) REVERT: D 11 LEU cc_start: 0.8384 (tp) cc_final: 0.8056 (mm) REVERT: D 93 ASN cc_start: 0.9134 (m-40) cc_final: 0.8773 (t0) REVERT: D 104 LYS cc_start: 0.9272 (tttt) cc_final: 0.9060 (tmtm) REVERT: K 128 LYS cc_start: 0.8832 (ptmm) cc_final: 0.8599 (ptmm) REVERT: C 10 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7402 (tm-30) REVERT: C 13 GLU cc_start: 0.8977 (mp0) cc_final: 0.8559 (pm20) REVERT: C 29 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: C 65 GLN cc_start: 0.8197 (tt0) cc_final: 0.7858 (mm-40) REVERT: C 74 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8107 (pm20) REVERT: C 102 ASP cc_start: 0.9315 (p0) cc_final: 0.9071 (p0) REVERT: I 13 LEU cc_start: 0.8623 (mt) cc_final: 0.8205 (tm) REVERT: I 24 ARG cc_start: 0.7383 (tmm-80) cc_final: 0.7087 (tmm-80) REVERT: I 35 TRP cc_start: 0.8349 (m100) cc_final: 0.7477 (m100) outliers start: 42 outliers final: 15 residues processed: 189 average time/residue: 1.5046 time to fit residues: 318.0290 Evaluate side-chains 158 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain 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 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 180 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19059 Z= 0.183 Angle : 0.642 8.345 25877 Z= 0.325 Chirality : 0.046 0.186 3096 Planarity : 0.004 0.042 3206 Dihedral : 7.197 53.570 4306 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 13.64 % 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: -0.50 (0.17), residues: 2252 helix: -0.69 (1.04), residues: 24 sheet: 0.37 (0.17), residues: 957 loop : -0.88 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.003 0.001 HIS J 336 PHE 0.013 0.002 PHE G 410 TYR 0.014 0.001 TYR F 49 ARG 0.008 0.000 ARG C 87 *********************** 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 200 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7803 (p90) cc_final: 0.7576 (m-70) REVERT: E 81 MET cc_start: 0.8270 (tmm) cc_final: 0.7908 (ppp) REVERT: E 86 LEU cc_start: 0.8471 (mt) cc_final: 0.8047 (mp) REVERT: F 1 GLU cc_start: 0.8009 (tt0) cc_final: 0.7739 (tp30) REVERT: F 61 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7879 (mtm110) REVERT: F 93 ASN cc_start: 0.9122 (m-40) cc_final: 0.8682 (t0) REVERT: F 109 ARG cc_start: 0.8116 (ptm160) cc_final: 0.6183 (ptp-170) REVERT: A 10 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7649 (mp0) REVERT: A 73 ASP cc_start: 0.8502 (t0) cc_final: 0.7908 (p0) REVERT: A 81 MET cc_start: 0.7650 (ttp) cc_final: 0.7219 (ttp) REVERT: D 1 GLU cc_start: 0.8032 (tt0) cc_final: 0.7585 (mm-30) REVERT: D 3 VAL cc_start: 0.9392 (t) cc_final: 0.9165 (m) REVERT: D 11 LEU cc_start: 0.8334 (tp) cc_final: 0.8032 (mm) REVERT: D 93 ASN cc_start: 0.9106 (m-40) cc_final: 0.8665 (t0) REVERT: D 104 LYS cc_start: 0.9253 (tttt) cc_final: 0.9019 (tmtm) REVERT: C 10 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7494 (tm-30) REVERT: C 13 GLU cc_start: 0.8983 (mp0) cc_final: 0.8564 (pm20) REVERT: C 29 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: C 65 GLN cc_start: 0.8162 (tt0) cc_final: 0.7802 (mm-40) REVERT: C 74 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8099 (pm20) REVERT: C 102 ASP cc_start: 0.9306 (p0) cc_final: 0.9046 (p0) REVERT: I 4 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: I 13 LEU cc_start: 0.8723 (mt) cc_final: 0.8314 (tm) REVERT: I 24 ARG cc_start: 0.7387 (tmm-80) cc_final: 0.7087 (tmm-80) REVERT: I 35 TRP cc_start: 0.8351 (m100) cc_final: 0.7457 (m100) outliers start: 47 outliers final: 23 residues processed: 191 average time/residue: 1.5349 time to fit residues: 328.0267 Evaluate side-chains 169 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 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 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 35 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain 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 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 72 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 226 GLN K 294 ASN L 226 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19059 Z= 0.332 Angle : 0.702 11.574 25877 Z= 0.357 Chirality : 0.048 0.234 3096 Planarity : 0.004 0.043 3206 Dihedral : 7.437 55.951 4306 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 14.26 % Favored : 83.48 % 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: -0.68 (0.17), residues: 2252 helix: -0.79 (1.01), residues: 24 sheet: 0.27 (0.17), residues: 953 loop : -1.02 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 178 HIS 0.006 0.001 HIS G 144 PHE 0.018 0.002 PHE J 354 TYR 0.020 0.002 TYR G 121 ARG 0.012 0.001 ARG F 45 *********************** 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 195 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 HIS cc_start: 0.7807 (p90) cc_final: 0.7587 (m-70) REVERT: E 86 LEU cc_start: 0.8521 (mt) cc_final: 0.8084 (mp) REVERT: F 82 ASP cc_start: 0.7486 (m-30) cc_final: 0.7283 (m-30) REVERT: F 93 ASN cc_start: 0.9152 (m-40) cc_final: 0.8704 (t0) REVERT: F 109 ARG cc_start: 0.8112 (ptm160) cc_final: 0.6239 (ptp-170) REVERT: A 10 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7673 (mp0) REVERT: A 81 MET cc_start: 0.7744 (ttp) cc_final: 0.7257 (ttp) REVERT: D 1 GLU cc_start: 0.8044 (tt0) cc_final: 0.7606 (mm-30) REVERT: D 3 VAL cc_start: 0.9460 (t) cc_final: 0.9246 (m) REVERT: D 11 LEU cc_start: 0.8401 (tp) cc_final: 0.8053 (mm) REVERT: D 37 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: D 93 ASN cc_start: 0.9177 (m-40) cc_final: 0.8701 (t0) REVERT: D 104 LYS cc_start: 0.9277 (tttt) cc_final: 0.9036 (tmtm) REVERT: D 109 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7149 (pmt170) REVERT: C 10 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7665 (tm-30) REVERT: C 13 GLU cc_start: 0.9005 (mp0) cc_final: 0.8602 (pm20) REVERT: C 29 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7322 (m-10) REVERT: C 65 GLN cc_start: 0.8280 (tt0) cc_final: 0.7996 (mm-40) REVERT: C 74 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8115 (pm20) REVERT: C 102 ASP cc_start: 0.9375 (p0) cc_final: 0.9129 (p0) REVERT: I 4 MET cc_start: 0.8650 (mmm) cc_final: 0.8025 (mmm) REVERT: I 13 LEU cc_start: 0.8840 (mt) cc_final: 0.8462 (tm) REVERT: I 24 ARG cc_start: 0.7453 (tmm-80) cc_final: 0.7156 (tmm-80) REVERT: I 35 TRP cc_start: 0.8398 (m100) cc_final: 0.7521 (m100) outliers start: 44 outliers final: 22 residues processed: 190 average time/residue: 1.5099 time to fit residues: 319.0515 Evaluate side-chains 163 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 CYS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 215 VAL 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 D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 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 29 PHE 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 208 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19059 Z= 0.201 Angle : 0.658 13.061 25877 Z= 0.333 Chirality : 0.046 0.199 3096 Planarity : 0.004 0.050 3206 Dihedral : 6.936 50.554 4306 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer: Outliers : 2.11 % Allowed : 14.77 % 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: -0.57 (0.17), residues: 2252 helix: -0.71 (1.05), residues: 24 sheet: 0.32 (0.17), residues: 961 loop : -0.93 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 PHE 0.015 0.002 PHE G 410 TYR 0.013 0.001 TYR E 80 ARG 0.012 0.000 ARG I 54 *********************** 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 191 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 2.056 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: 0.7847 (OUTLIER) cc_final: 0.7605 (m-70) REVERT: E 86 LEU cc_start: 0.8525 (mt) cc_final: 0.8122 (mp) REVERT: F 93 ASN cc_start: 0.9124 (m-40) cc_final: 0.8679 (t0) REVERT: F 109 ARG cc_start: 0.8109 (ptm160) cc_final: 0.6365 (ptp-170) REVERT: A 10 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 81 MET cc_start: 0.7741 (ttp) cc_final: 0.7229 (ttp) REVERT: D 1 GLU cc_start: 0.8058 (tt0) cc_final: 0.7632 (mm-30) REVERT: D 11 LEU cc_start: 0.8371 (tp) cc_final: 0.8028 (mm) REVERT: D 37 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: D 93 ASN cc_start: 0.9131 (m-40) cc_final: 0.8660 (t0) REVERT: D 104 LYS cc_start: 0.9258 (tttt) cc_final: 0.9021 (tmtm) REVERT: D 106 GLU cc_start: 0.7586 (tp30) cc_final: 0.7343 (tp30) REVERT: D 109 ARG cc_start: 0.7800 (ptm160) cc_final: 0.7141 (pmt170) REVERT: C 10 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7712 (tm-30) REVERT: C 13 GLU cc_start: 0.8982 (mp0) cc_final: 0.8576 (pm20) REVERT: C 29 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: C 65 GLN cc_start: 0.8176 (tt0) cc_final: 0.7935 (mm-40) REVERT: C 74 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8056 (pm20) REVERT: C 102 ASP cc_start: 0.9348 (p0) cc_final: 0.9083 (p0) REVERT: I 4 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: I 13 LEU cc_start: 0.8862 (mt) cc_final: 0.8480 (tm) REVERT: I 24 ARG cc_start: 0.7463 (tmm-80) cc_final: 0.7196 (tmm-80) REVERT: I 35 TRP cc_start: 0.8437 (m100) cc_final: 0.7550 (m100) REVERT: I 75 ILE cc_start: 0.9182 (mt) cc_final: 0.8713 (tp) outliers start: 41 outliers final: 17 residues processed: 185 average time/residue: 1.5544 time to fit residues: 319.3110 Evaluate side-chains 160 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 128 LYS Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 230 CYS Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 230 CYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain I residue 4 MET 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 133 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 0.0370 chunk 20 optimal weight: 0.0170 chunk 169 optimal weight: 2.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN G 441 ASN E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 92 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 19059 Z= 0.157 Angle : 0.637 12.254 25877 Z= 0.323 Chirality : 0.045 0.190 3096 Planarity : 0.004 0.048 3206 Dihedral : 6.473 45.419 4306 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 1.80 % Allowed : 15.54 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.87 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (1.01), residues: 24 sheet: 0.45 (0.17), residues: 937 loop : -0.81 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 178 HIS 0.003 0.000 HIS C 3 PHE 0.014 0.001 PHE G 410 TYR 0.019 0.001 TYR F 49 ARG 0.012 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 241 MET cc_start: 0.8775 (mtp) cc_final: 0.8290 (mtm) REVERT: G 362 MET cc_start: 0.8688 (ptm) cc_final: 0.8296 (ppp) REVERT: E 3 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7618 (m-70) REVERT: E 86 LEU cc_start: 0.8463 (mt) cc_final: 0.8075 (mp) REVERT: F 61 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7562 (ttp-170) REVERT: F 93 ASN cc_start: 0.9055 (m-40) cc_final: 0.8642 (t0) REVERT: F 109 ARG cc_start: 0.8057 (ptm160) cc_final: 0.6374 (ptp-170) REVERT: A 10 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 81 MET cc_start: 0.7710 (ttp) cc_final: 0.7253 (ttp) REVERT: D 1 GLU cc_start: 0.7996 (tt0) cc_final: 0.7605 (mm-30) REVERT: D 11 LEU cc_start: 0.8338 (tp) cc_final: 0.7988 (mm) REVERT: D 37 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: D 93 ASN cc_start: 0.9088 (m-40) cc_final: 0.8640 (t0) REVERT: D 104 LYS cc_start: 0.9266 (tttt) cc_final: 0.9026 (tmtm) REVERT: D 106 GLU cc_start: 0.7546 (tp30) cc_final: 0.7299 (tp30) REVERT: D 109 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7185 (pmt170) REVERT: C 10 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7747 (tm-30) REVERT: C 13 GLU cc_start: 0.8971 (mp0) cc_final: 0.8562 (pm20) REVERT: C 29 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: C 74 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8035 (pm20) REVERT: C 102 ASP cc_start: 0.9298 (p0) cc_final: 0.9041 (p0) REVERT: C 111 GLU cc_start: 0.8766 (tp30) cc_final: 0.8499 (tp30) REVERT: I 4 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8204 (mmm) REVERT: I 13 LEU cc_start: 0.8867 (mt) cc_final: 0.8484 (tm) REVERT: I 24 ARG cc_start: 0.7341 (tmm-80) cc_final: 0.7000 (tmm160) REVERT: I 35 TRP cc_start: 0.8420 (m100) cc_final: 0.7521 (m100) REVERT: I 75 ILE cc_start: 0.9180 (mt) cc_final: 0.8719 (tp) outliers start: 35 outliers final: 13 residues processed: 180 average time/residue: 1.4763 time to fit residues: 296.8437 Evaluate side-chains 156 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 318 CYS Chi-restraints excluded: chain 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 230 CYS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain I residue 4 MET 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 196 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 201 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 87 optimal weight: 0.0270 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19059 Z= 0.208 Angle : 0.660 12.505 25877 Z= 0.334 Chirality : 0.046 0.193 3096 Planarity : 0.004 0.054 3206 Dihedral : 6.482 44.778 4306 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer: Outliers : 1.39 % Allowed : 16.52 % Favored : 82.09 % 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: -0.43 (0.17), residues: 2252 helix: -0.68 (1.04), residues: 24 sheet: 0.48 (0.17), residues: 931 loop : -0.85 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 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 0.013 0.001 ARG C 87 *********************** 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 167 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 362 MET cc_start: 0.8730 (ptm) cc_final: 0.8342 (ppp) REVERT: E 63 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8348 (ptm-80) REVERT: E 86 LEU cc_start: 0.8474 (mt) cc_final: 0.8055 (mp) REVERT: F 61 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7533 (ttp-170) REVERT: F 81 GLU cc_start: 0.8511 (pm20) cc_final: 0.8309 (pm20) REVERT: F 82 ASP cc_start: 0.7732 (m-30) cc_final: 0.6795 (m-30) REVERT: F 93 ASN cc_start: 0.9085 (m-40) cc_final: 0.8657 (t0) REVERT: F 109 ARG cc_start: 0.8043 (ptm160) cc_final: 0.6388 (ptp-170) REVERT: A 10 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7812 (mp0) REVERT: D 1 GLU cc_start: 0.8000 (tt0) cc_final: 0.7615 (mm-30) REVERT: D 11 LEU cc_start: 0.8354 (tp) cc_final: 0.7999 (mm) REVERT: D 37 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: D 81 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8557 (tp30) REVERT: D 93 ASN cc_start: 0.9107 (m-40) cc_final: 0.8655 (t0) REVERT: D 104 LYS cc_start: 0.9266 (tttt) cc_final: 0.9033 (tmtm) REVERT: D 106 GLU cc_start: 0.7554 (tp30) cc_final: 0.7322 (tp30) REVERT: D 109 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7215 (pmt170) REVERT: C 10 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7809 (tm-30) REVERT: C 13 GLU cc_start: 0.8961 (mp0) cc_final: 0.8549 (pm20) REVERT: C 29 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: C 65 GLN cc_start: 0.8047 (tt0) cc_final: 0.7811 (mm-40) REVERT: C 74 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8029 (pm20) REVERT: C 102 ASP cc_start: 0.9305 (p0) cc_final: 0.9050 (p0) REVERT: I 13 LEU cc_start: 0.8890 (mt) cc_final: 0.8512 (tm) REVERT: I 24 ARG cc_start: 0.7389 (tmm-80) cc_final: 0.7085 (tmm160) REVERT: I 35 TRP cc_start: 0.8425 (m100) cc_final: 0.7552 (m100) REVERT: I 75 ILE cc_start: 0.9212 (mt) cc_final: 0.8763 (tp) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 1.5740 time to fit residues: 279.1884 Evaluate side-chains 153 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 318 CYS 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 230 CYS Chi-restraints excluded: chain C residue 29 PHE 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 132 optimal weight: 0.2980 chunk 212 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 294 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 HIS A 62 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19059 Z= 0.219 Angle : 0.665 12.423 25877 Z= 0.337 Chirality : 0.046 0.193 3096 Planarity : 0.004 0.051 3206 Dihedral : 6.482 44.609 4306 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 1.44 % Allowed : 16.68 % Favored : 81.88 % 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: -0.49 (0.17), residues: 2252 helix: -0.69 (1.03), residues: 24 sheet: 0.41 (0.17), residues: 913 loop : -0.86 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 PHE 0.015 0.002 PHE G 410 TYR 0.020 0.001 TYR F 49 ARG 0.014 0.001 ARG C 87 ********************** 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: 28 poor density : 137 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8622 (mtpp) REVERT: E 86 LEU cc_start: 0.8491 (mt) cc_final: 0.8079 (mp) REVERT: F 24 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8042 (mpp80) REVERT: F 61 ARG cc_start: 0.8317 (mtm110) cc_final: 0.7499 (ttp-170) REVERT: F 81 GLU cc_start: 0.8479 (pm20) cc_final: 0.8263 (pm20) REVERT: F 82 ASP cc_start: 0.7640 (m-30) cc_final: 0.6626 (m-30) REVERT: F 93 ASN cc_start: 0.9093 (m-40) cc_final: 0.8644 (t0) REVERT: F 109 ARG cc_start: 0.7984 (ptm160) cc_final: 0.6378 (ptp-170) REVERT: A 10 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7795 (mp0) REVERT: D 1 GLU cc_start: 0.8015 (tt0) cc_final: 0.7340 (tm-30) REVERT: D 11 LEU cc_start: 0.8353 (tp) cc_final: 0.8000 (mm) REVERT: D 37 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: D 81 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8528 (tp30) REVERT: D 93 ASN cc_start: 0.9133 (m-40) cc_final: 0.8676 (t0) REVERT: D 104 LYS cc_start: 0.9265 (tttt) cc_final: 0.9035 (tmtm) REVERT: D 106 GLU cc_start: 0.7586 (tp30) cc_final: 0.7346 (tp30) REVERT: D 109 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7218 (pmt170) REVERT: C 10 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7790 (tm-30) REVERT: C 13 GLU cc_start: 0.8959 (mp0) cc_final: 0.8555 (pm20) REVERT: C 29 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: C 65 GLN cc_start: 0.8066 (tt0) cc_final: 0.7727 (mm110) REVERT: C 74 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8031 (pm20) REVERT: C 102 ASP cc_start: 0.9339 (p0) cc_final: 0.9083 (p0) REVERT: I 13 LEU cc_start: 0.8921 (mt) cc_final: 0.8552 (tm) REVERT: I 24 ARG cc_start: 0.7487 (tmm-80) cc_final: 0.7175 (tmm160) REVERT: I 35 TRP cc_start: 0.8455 (m100) cc_final: 0.7548 (m100) REVERT: I 75 ILE cc_start: 0.9228 (mt) cc_final: 0.8752 (tp) outliers start: 28 outliers final: 13 residues processed: 160 average time/residue: 1.5927 time to fit residues: 284.4878 Evaluate side-chains 148 residues out of total 1943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain 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 230 CYS Chi-restraints excluded: chain C residue 29 PHE 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 141 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 HIS A 62 GLN ** 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 = 0.3649 r_free = 0.3649 target = 0.096184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067241 restraints weight = 37324.540| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.14 r_work: 0.2956 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19059 Z= 0.208 Angle : 0.666 12.255 25877 Z= 0.338 Chirality : 0.046 0.194 3096 Planarity : 0.004 0.050 3206 Dihedral : 6.411 44.125 4306 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 1.13 % Allowed : 16.88 % Favored : 81.99 % 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: -0.71 (1.02), residues: 24 sheet: 0.42 (0.17), residues: 913 loop : -0.90 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 178 HIS 0.003 0.001 HIS C 3 PHE 0.015 0.002 PHE G 410 TYR 0.018 0.001 TYR A 80 ARG 0.013 0.000 ARG C 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6271.03 seconds wall clock time: 113 minutes 56.84 seconds (6836.84 seconds total)