Starting phenix.real_space_refine on Wed Nov 20 00:32:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3n_29705/11_2024/8g3n_29705.cif" } resolution = 2.9 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 116 5.16 5 C 12564 2.51 5 N 3434 2.21 5 O 4202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20321 Number of models: 1 Model: "" Number of chains: 39 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: "B" 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: "H" 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: "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: 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: "r" 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: "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: 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: "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: 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: "P" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 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: "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: "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: 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: "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: 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: "R" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.53, per 1000 atoms: 0.67 Number of scatterers: 20321 At special positions: 0 Unit cell: (149.741, 149.741, 106.021, 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 116 16.00 O 4202 8.00 N 3434 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.05 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.10 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.10 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.13 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.09 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.09 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.15 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.09 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.22 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.07 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.08 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.10 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.10 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.13 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.09 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.09 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.15 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.22 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.07 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.08 Simple disulfide: pdb=" SG CYS K 92 " - pdb=" SG CYS K 417 " distance=2.05 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 129 " distance=2.10 Simple disulfide: pdb=" SG CYS K 175 " - pdb=" SG CYS K 193 " distance=2.10 Simple disulfide: pdb=" SG CYS K 183 " - pdb=" SG CYS K 230 " distance=2.13 Simple disulfide: pdb=" SG CYS K 232 " - pdb=" SG CYS K 237 " distance=2.09 Simple disulfide: pdb=" SG CYS K 278 " - pdb=" SG CYS K 291 " distance=2.09 Simple disulfide: pdb=" SG CYS K 280 " - pdb=" SG CYS K 289 " distance=2.15 Simple disulfide: pdb=" SG CYS K 318 " - pdb=" SG CYS K 337 " distance=2.09 Simple disulfide: pdb=" SG CYS K 421 " - pdb=" SG CYS K 447 " distance=2.22 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.08 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=2.10 Simple disulfide: pdb=" SG CYS L 175 " - pdb=" SG CYS L 193 " distance=2.10 Simple disulfide: pdb=" SG CYS L 183 " - pdb=" SG CYS L 230 " distance=2.13 Simple disulfide: pdb=" SG CYS L 232 " - pdb=" SG CYS L 237 " distance=2.09 Simple disulfide: pdb=" SG CYS L 278 " - pdb=" SG CYS L 291 " distance=2.09 Simple disulfide: pdb=" SG CYS L 280 " - pdb=" SG CYS L 289 " distance=2.15 Simple disulfide: pdb=" SG CYS L 318 " - pdb=" SG CYS L 337 " distance=2.09 Simple disulfide: pdb=" SG CYS L 421 " - pdb=" SG CYS L 447 " distance=2.22 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.07 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.08 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 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 s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 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 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 v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG V 1 " - " FUC V 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " 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 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: 6.52 Conformation dependent library (CDL) restraints added in 3.0 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4552 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 44 sheets defined 4.1% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.595A 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: 3.688A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 removed outlier: 3.614A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.596A 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: 3.690A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.595A pdb=" N ASN K 146 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.689A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 110 removed outlier: 3.615A pdb=" N ALA L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.595A 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: 3.689A 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: 3.621A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.893A 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: 4.860A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.053A 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: 3.620A pdb=" N SER G 179 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.264A 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: 3.734A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.477A 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: 5.435A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.841A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY G 363 " --> pdb=" O TRP G 352 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.792A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.886A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.487A 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: 6.454A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.708A 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: 6.454A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU F 13 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.594A 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: 3.622A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.893A 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: 4.860A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 4.053A 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: 3.620A pdb=" N SER J 179 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.264A 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: 3.736A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.476A 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: 5.436A 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 352 through 356 removed outlier: 4.842A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY J 363 " --> pdb=" O TRP J 352 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.484A 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: 6.458A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.706A 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: 6.458A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 117 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU D 13 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.595A 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: 3.621A pdb=" N GLY K 96 " --> pdb=" O THR K 449 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL K 445 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS K 102 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE K 443 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.894A 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: 4.861A pdb=" N TRP K 115 " --> pdb=" O THR K 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR K 138 " --> pdb=" O TRP K 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN K 136 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR K 157 " --> pdb=" O GLY K 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 158 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 4.052A 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: 3.620A pdb=" N SER K 179 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP K 197 " --> pdb=" O ASN K 200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 213 " --> pdb=" O PHE K 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR K 207 " --> pdb=" O LEU K 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU K 211 " --> pdb=" O TYR K 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 231 through 233 removed outlier: 3.735A pdb=" N VAL K 231 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU K 258 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE K 262 " --> pdb=" O GLU K 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 276 through 283 removed outlier: 5.435A pdb=" N GLU K 277 " --> pdb=" O ARG K 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG K 292 " --> pdb=" O GLU K 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 352 through 356 removed outlier: 4.841A pdb=" N TRP K 352 " --> pdb=" O GLY K 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY K 363 " --> pdb=" O TRP K 352 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN K 402 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU K 375 " --> pdb=" O ARG K 400 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N ARG K 400 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 11.644A pdb=" N PHE K 377 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N VAL K 398 " --> pdb=" O PHE K 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL K 379 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 16.485A pdb=" N VAL K 396 " --> pdb=" O VAL K 379 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.453A pdb=" N GLU B 10 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.453A pdb=" N GLU B 10 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS B 96 " --> pdb=" O TRP B 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP B 118 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 98 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.648A pdb=" N LEU H 13 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 96 through 102 removed outlier: 3.621A pdb=" N GLY L 96 " --> pdb=" O THR L 449 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL L 445 " --> pdb=" O PHE L 100 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS L 102 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE L 443 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG L 420 " --> pdb=" O GLY L 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 115 through 124 removed outlier: 4.860A pdb=" N TRP L 115 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR L 138 " --> pdb=" O TRP L 115 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR L 117 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN L 136 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU L 119 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU L 134 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 157 " --> pdb=" O GLY L 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 158 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS L 172 " --> pdb=" O MET L 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 179 through 184 removed outlier: 3.620A pdb=" N SER L 179 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP L 197 " --> pdb=" O ASN L 200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP L 213 " --> pdb=" O PHE L 205 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR L 207 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU L 211 " --> pdb=" O TYR L 207 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 231 through 233 removed outlier: 3.735A pdb=" N VAL L 231 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU L 258 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 276 through 283 removed outlier: 5.435A pdb=" N GLU L 277 " --> pdb=" O ARG L 292 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG L 292 " --> pdb=" O GLU L 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 352 through 356 removed outlier: 4.842A pdb=" N TRP L 352 " --> pdb=" O GLY L 363 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY L 363 " --> pdb=" O TRP L 352 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN L 402 " --> pdb=" O GLY L 373 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLU L 375 " --> pdb=" O ARG L 400 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N ARG L 400 " --> pdb=" O GLU L 375 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N PHE L 377 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N VAL L 398 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N VAL L 379 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 16.485A pdb=" N VAL L 396 " --> pdb=" O VAL L 379 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.454A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.647A pdb=" N LEU I 13 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3289 1.30 - 1.44: 5731 1.44 - 1.57: 11592 1.57 - 1.70: 0 1.70 - 1.84: 144 Bond restraints: 20756 Sorted by residual: bond pdb=" CE1 HIS L 184 " pdb=" NE2 HIS L 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" CE1 HIS K 184 " pdb=" NE2 HIS K 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CE1 HIS G 184 " pdb=" NE2 HIS G 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CE1 HIS J 184 " pdb=" NE2 HIS J 184 " ideal model delta sigma weight residual 1.321 1.254 0.067 1.00e-02 1.00e+04 4.42e+01 bond pdb=" C VAL J 317 " pdb=" O VAL J 317 " ideal model delta sigma weight residual 1.237 1.299 -0.062 9.90e-03 1.02e+04 3.91e+01 ... (remaining 20751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 19634 1.71 - 3.41: 6846 3.41 - 5.12: 1506 5.12 - 6.82: 160 6.82 - 8.53: 36 Bond angle restraints: 28182 Sorted by residual: angle pdb=" CA ASP L 125 " pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" CA ASP J 125 " pdb=" CB ASP J 125 " pdb=" CG ASP J 125 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP K 125 " pdb=" CB ASP K 125 " pdb=" CG ASP K 125 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" N SER K 180 " pdb=" CA SER K 180 " pdb=" C SER K 180 " ideal model delta sigma weight residual 108.60 116.46 -7.86 1.46e+00 4.69e-01 2.90e+01 ... (remaining 28177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 12551 21.62 - 43.23: 535 43.23 - 64.85: 85 64.85 - 86.47: 61 86.47 - 108.08: 28 Dihedral angle restraints: 13260 sinusoidal: 6116 harmonic: 7144 Sorted by residual: dihedral pdb=" CA VAL A 2 " pdb=" C VAL A 2 " pdb=" N HIS A 3 " pdb=" CA HIS A 3 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA VAL B 2 " pdb=" C VAL B 2 " pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta harmonic sigma weight residual 180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL C 2 " pdb=" C VAL C 2 " pdb=" N HIS C 3 " pdb=" CA HIS C 3 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 13257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1382 0.055 - 0.110: 1063 0.110 - 0.164: 602 0.164 - 0.219: 179 0.219 - 0.274: 66 Chirality restraints: 3292 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.28e+01 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.97e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.95e+01 ... (remaining 3289 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP J 115 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP J 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP J 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP J 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.13e+01 pdb=" CG TRP K 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP K 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP K 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP K 115 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP K 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP K 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 115 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP K 115 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 115 " 0.113 2.00e-02 2.50e+03 5.34e-02 7.12e+01 pdb=" CG TRP G 115 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 115 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP G 115 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP G 115 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 115 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 115 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP G 115 " 0.051 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3843 2.82 - 3.34: 18780 3.34 - 3.86: 32203 3.86 - 4.38: 41311 4.38 - 4.90: 68081 Nonbonded interactions: 164218 Sorted by model distance: nonbonded pdb=" O HIS L 347 " pdb="CA CA L2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS K 347 " pdb="CA CA K2000 " model vdw 2.302 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.303 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.303 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J2000 " model vdw 2.342 2.510 ... (remaining 164213 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 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 501)) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'q' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 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: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 50.260 Find NCS groups from input model: 1.170 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:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 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 0.072 20756 Z= 1.067 Angle : 1.755 8.529 28182 Z= 1.145 Chirality : 0.095 0.274 3292 Planarity : 0.011 0.068 3534 Dihedral : 14.521 108.083 8576 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.63 (0.15), residues: 2488 helix: -1.68 (0.62), residues: 24 sheet: 0.32 (0.16), residues: 980 loop : -0.92 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.014 TRP J 115 HIS 0.032 0.005 HIS L 168 PHE 0.062 0.012 PHE L 205 TYR 0.058 0.012 TYR J 121 ARG 0.022 0.004 ARG L 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 2.237 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ASP cc_start: 0.7076 (t0) cc_final: 0.6734 (t0) REVERT: F 85 ILE cc_start: 0.8678 (tt) cc_final: 0.8461 (tp) REVERT: A 10 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8290 (tp30) REVERT: A 13 GLU cc_start: 0.9044 (mp0) cc_final: 0.8835 (pm20) REVERT: A 73 ASP cc_start: 0.7079 (t0) cc_final: 0.6737 (t0) REVERT: D 85 ILE cc_start: 0.8673 (tt) cc_final: 0.8458 (tp) REVERT: B 73 ASP cc_start: 0.7074 (t0) cc_final: 0.6732 (t0) REVERT: H 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8461 (tp) REVERT: C 73 ASP cc_start: 0.7071 (t0) cc_final: 0.6728 (t0) REVERT: I 85 ILE cc_start: 0.8677 (tt) cc_final: 0.8461 (tp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 1.8203 time to fit residues: 552.8605 Evaluate side-chains 204 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 ASN E 39 GLN E 43 GLN F 93 ASN J 147 ASN A 39 GLN A 43 GLN D 93 ASN K 147 ASN B 39 GLN B 43 GLN H 93 ASN L 147 ASN C 39 GLN C 43 GLN I 93 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20756 Z= 0.220 Angle : 0.693 8.061 28182 Z= 0.365 Chirality : 0.048 0.162 3292 Planarity : 0.004 0.053 3534 Dihedral : 10.048 73.994 4264 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 2.20 % Allowed : 9.86 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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 (0.16), residues: 2488 helix: -0.18 (0.98), residues: 24 sheet: 0.25 (0.15), residues: 1092 loop : -0.70 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 178 HIS 0.005 0.002 HIS G 347 PHE 0.014 0.002 PHE J 410 TYR 0.013 0.002 TYR F 49 ARG 0.007 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 2.691 Fit side-chains revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8625 (mp0) REVERT: E 23 LYS cc_start: 0.9051 (tttp) cc_final: 0.8850 (tttp) REVERT: E 65 GLN cc_start: 0.8633 (tt0) cc_final: 0.8199 (mt0) REVERT: E 73 ASP cc_start: 0.7656 (t0) cc_final: 0.7168 (t0) REVERT: F 6 GLN cc_start: 0.8515 (tt0) cc_final: 0.8215 (tt0) REVERT: F 61 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7734 (ptm160) REVERT: F 79 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8057 (mp-120) REVERT: F 81 GLU cc_start: 0.8959 (pm20) cc_final: 0.8734 (pm20) REVERT: F 82 ASP cc_start: 0.8672 (m-30) cc_final: 0.7896 (m-30) REVERT: F 106 GLU cc_start: 0.6275 (tm-30) cc_final: 0.6008 (tm-30) REVERT: A 10 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8534 (tp30) REVERT: A 65 GLN cc_start: 0.8608 (tt0) cc_final: 0.8167 (mt0) REVERT: A 73 ASP cc_start: 0.7655 (t0) cc_final: 0.7166 (t0) REVERT: D 6 GLN cc_start: 0.8491 (tt0) cc_final: 0.8203 (tt0) REVERT: D 61 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7819 (ptm160) REVERT: D 79 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8066 (mp-120) REVERT: D 81 GLU cc_start: 0.8958 (pm20) cc_final: 0.8736 (pm20) REVERT: D 82 ASP cc_start: 0.8652 (m-30) cc_final: 0.7869 (m-30) REVERT: D 106 GLU cc_start: 0.6272 (tm-30) cc_final: 0.6007 (tm-30) REVERT: K 160 MET cc_start: 0.8788 (ttt) cc_final: 0.8582 (ttt) REVERT: B 10 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8621 (mp0) REVERT: B 23 LYS cc_start: 0.9051 (tttp) cc_final: 0.8850 (tttp) REVERT: B 65 GLN cc_start: 0.8625 (tt0) cc_final: 0.8192 (mt0) REVERT: B 73 ASP cc_start: 0.7655 (t0) cc_final: 0.7166 (t0) REVERT: H 6 GLN cc_start: 0.8513 (tt0) cc_final: 0.8198 (tt0) REVERT: H 61 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7734 (ptm160) REVERT: H 79 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8050 (mp-120) REVERT: H 81 GLU cc_start: 0.8960 (pm20) cc_final: 0.8734 (pm20) REVERT: H 82 ASP cc_start: 0.8670 (m-30) cc_final: 0.7890 (m-30) REVERT: H 106 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5888 (tm-30) REVERT: C 10 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8619 (mp0) REVERT: C 23 LYS cc_start: 0.9053 (tttp) cc_final: 0.8851 (tttp) REVERT: C 65 GLN cc_start: 0.8624 (tt0) cc_final: 0.8198 (mt0) REVERT: C 73 ASP cc_start: 0.7655 (t0) cc_final: 0.7167 (t0) REVERT: I 6 GLN cc_start: 0.8514 (tt0) cc_final: 0.8215 (tt0) REVERT: I 61 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7730 (ptm160) REVERT: I 79 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8064 (mp-120) REVERT: I 81 GLU cc_start: 0.8960 (pm20) cc_final: 0.8735 (pm20) REVERT: I 82 ASP cc_start: 0.8652 (m-30) cc_final: 0.7876 (m-30) outliers start: 47 outliers final: 4 residues processed: 251 average time/residue: 1.7459 time to fit residues: 485.1034 Evaluate side-chains 210 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 93 ASN A 39 GLN D 93 ASN B 39 GLN H 93 ASN C 39 GLN I 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20756 Z= 0.286 Angle : 0.662 7.629 28182 Z= 0.341 Chirality : 0.048 0.167 3292 Planarity : 0.005 0.054 3534 Dihedral : 8.428 62.523 4264 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 3.08 % Allowed : 9.72 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.45 (0.16), residues: 2488 helix: 0.04 (1.11), residues: 24 sheet: 0.32 (0.15), residues: 1080 loop : -0.78 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 178 HIS 0.006 0.002 HIS L 184 PHE 0.014 0.002 PHE J 410 TYR 0.020 0.002 TYR K 121 ARG 0.010 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 2.393 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: symmetry clash REVERT: E 10 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8742 (mp0) REVERT: E 23 LYS cc_start: 0.9096 (tttp) cc_final: 0.8807 (tttp) REVERT: E 65 GLN cc_start: 0.8634 (tt0) cc_final: 0.8213 (mt0) REVERT: E 73 ASP cc_start: 0.7651 (t0) cc_final: 0.7120 (t0) REVERT: E 77 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8533 (p) REVERT: F 82 ASP cc_start: 0.8784 (m-30) cc_final: 0.8304 (m-30) REVERT: A 10 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8717 (tp30) REVERT: A 23 LYS cc_start: 0.9112 (tttp) cc_final: 0.8781 (tttp) REVERT: A 65 GLN cc_start: 0.8622 (tt0) cc_final: 0.8220 (mm-40) REVERT: A 73 ASP cc_start: 0.7657 (t0) cc_final: 0.7151 (t0) REVERT: A 77 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8304 (p) REVERT: D 81 GLU cc_start: 0.9047 (pm20) cc_final: 0.8846 (pm20) REVERT: D 82 ASP cc_start: 0.8764 (m-30) cc_final: 0.8235 (m-30) REVERT: B 10 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8734 (mp0) REVERT: B 23 LYS cc_start: 0.9098 (tttp) cc_final: 0.8811 (tttp) REVERT: B 65 GLN cc_start: 0.8626 (tt0) cc_final: 0.8197 (mt0) REVERT: B 73 ASP cc_start: 0.7652 (t0) cc_final: 0.7121 (t0) REVERT: B 77 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8530 (p) REVERT: H 82 ASP cc_start: 0.8785 (m-30) cc_final: 0.8300 (m-30) REVERT: C 10 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8735 (mp0) REVERT: C 23 LYS cc_start: 0.9099 (tttp) cc_final: 0.8811 (tttp) REVERT: C 65 GLN cc_start: 0.8624 (tt0) cc_final: 0.8202 (mt0) REVERT: C 73 ASP cc_start: 0.7650 (t0) cc_final: 0.7122 (t0) REVERT: C 77 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8497 (p) REVERT: I 82 ASP cc_start: 0.8764 (m-30) cc_final: 0.8271 (m-30) outliers start: 66 outliers final: 16 residues processed: 258 average time/residue: 1.6900 time to fit residues: 484.1082 Evaluate side-chains 222 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 0.0470 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20756 Z= 0.218 Angle : 0.622 7.502 28182 Z= 0.319 Chirality : 0.046 0.181 3292 Planarity : 0.004 0.045 3534 Dihedral : 7.410 58.711 4264 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.07 % Rotamer: Outliers : 2.85 % Allowed : 10.70 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.29 (0.16), residues: 2488 helix: -0.15 (1.05), residues: 24 sheet: 0.47 (0.16), residues: 1072 loop : -0.71 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 178 HIS 0.003 0.001 HIS K 347 PHE 0.013 0.002 PHE L 410 TYR 0.014 0.001 TYR K 121 ARG 0.009 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 2.315 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 10 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8801 (mp0) REVERT: E 23 LYS cc_start: 0.9107 (tttp) cc_final: 0.8809 (tttp) REVERT: E 65 GLN cc_start: 0.8549 (tt0) cc_final: 0.8179 (mm-40) REVERT: E 73 ASP cc_start: 0.7710 (t0) cc_final: 0.7158 (t0) REVERT: E 77 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8542 (p) REVERT: E 107 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8740 (m-30) REVERT: F 11 LEU cc_start: 0.8458 (tp) cc_final: 0.8230 (tt) REVERT: F 82 ASP cc_start: 0.8847 (m-30) cc_final: 0.8563 (m-30) REVERT: A 10 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8750 (tp30) REVERT: A 23 LYS cc_start: 0.9109 (tttp) cc_final: 0.8630 (tttp) REVERT: A 65 GLN cc_start: 0.8512 (tt0) cc_final: 0.8108 (mm-40) REVERT: A 73 ASP cc_start: 0.7708 (t0) cc_final: 0.7161 (t0) REVERT: A 77 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 87 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7899 (ptp-110) REVERT: D 11 LEU cc_start: 0.8455 (tp) cc_final: 0.8231 (tt) REVERT: D 81 GLU cc_start: 0.9070 (pm20) cc_final: 0.8790 (pm20) REVERT: D 82 ASP cc_start: 0.8771 (m-30) cc_final: 0.8054 (m-30) REVERT: B 10 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8796 (mp0) REVERT: B 23 LYS cc_start: 0.9111 (tttp) cc_final: 0.8816 (tttp) REVERT: B 65 GLN cc_start: 0.8534 (tt0) cc_final: 0.8141 (mm-40) REVERT: B 73 ASP cc_start: 0.7705 (t0) cc_final: 0.7152 (t0) REVERT: B 77 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 107 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8739 (m-30) REVERT: H 11 LEU cc_start: 0.8454 (tp) cc_final: 0.8231 (tt) REVERT: H 82 ASP cc_start: 0.8845 (m-30) cc_final: 0.8560 (m-30) REVERT: C 10 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8798 (mp0) REVERT: C 23 LYS cc_start: 0.9109 (tttp) cc_final: 0.8810 (tttp) REVERT: C 65 GLN cc_start: 0.8534 (tt0) cc_final: 0.8148 (mm-40) REVERT: C 73 ASP cc_start: 0.7710 (t0) cc_final: 0.7158 (t0) REVERT: C 77 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 107 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8739 (m-30) REVERT: I 11 LEU cc_start: 0.8473 (tp) cc_final: 0.8244 (tt) REVERT: I 82 ASP cc_start: 0.8814 (m-30) cc_final: 0.8531 (m-30) outliers start: 61 outliers final: 11 residues processed: 257 average time/residue: 1.7014 time to fit residues: 484.1703 Evaluate side-chains 226 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 6 GLN D 6 GLN B 39 GLN H 6 GLN C 39 GLN I 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20756 Z= 0.266 Angle : 0.639 8.200 28182 Z= 0.325 Chirality : 0.046 0.184 3292 Planarity : 0.005 0.046 3534 Dihedral : 7.145 55.489 4264 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 2.57 % Allowed : 11.21 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.30 (0.16), residues: 2488 helix: -0.19 (1.06), residues: 24 sheet: 0.48 (0.16), residues: 1072 loop : -0.74 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 178 HIS 0.004 0.001 HIS J 184 PHE 0.014 0.002 PHE L 410 TYR 0.019 0.001 TYR F 49 ARG 0.011 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 2.280 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 10 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8815 (mp0) REVERT: E 23 LYS cc_start: 0.9132 (tttp) cc_final: 0.8837 (tttp) REVERT: E 39 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: E 65 GLN cc_start: 0.8637 (tt0) cc_final: 0.8211 (mm-40) REVERT: E 73 ASP cc_start: 0.7729 (t0) cc_final: 0.7162 (t0) REVERT: E 77 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8525 (p) REVERT: E 87 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7913 (ptp-110) REVERT: F 11 LEU cc_start: 0.8500 (tp) cc_final: 0.8263 (tt) REVERT: F 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.8483 (m-30) REVERT: A 10 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8753 (tp30) REVERT: A 23 LYS cc_start: 0.9117 (tttp) cc_final: 0.8720 (tttp) REVERT: A 46 GLU cc_start: 0.9141 (tt0) cc_final: 0.8917 (tt0) REVERT: A 65 GLN cc_start: 0.8594 (tt0) cc_final: 0.8207 (mm-40) REVERT: A 73 ASP cc_start: 0.7731 (t0) cc_final: 0.7168 (t0) REVERT: A 77 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8592 (p) REVERT: D 11 LEU cc_start: 0.8480 (tp) cc_final: 0.8240 (tt) REVERT: D 81 GLU cc_start: 0.9051 (pm20) cc_final: 0.8777 (pm20) REVERT: D 82 ASP cc_start: 0.8737 (m-30) cc_final: 0.8051 (m-30) REVERT: B 10 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8823 (mp0) REVERT: B 23 LYS cc_start: 0.9133 (tttp) cc_final: 0.8832 (tttp) REVERT: B 39 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: B 65 GLN cc_start: 0.8609 (tt0) cc_final: 0.8166 (mm-40) REVERT: B 73 ASP cc_start: 0.7724 (t0) cc_final: 0.7152 (t0) REVERT: B 77 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (p) REVERT: H 11 LEU cc_start: 0.8496 (tp) cc_final: 0.8262 (tt) REVERT: H 82 ASP cc_start: 0.8748 (m-30) cc_final: 0.8451 (m-30) REVERT: C 10 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8824 (mp0) REVERT: C 23 LYS cc_start: 0.9134 (tttp) cc_final: 0.8831 (tttp) REVERT: C 39 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: C 65 GLN cc_start: 0.8609 (tt0) cc_final: 0.8173 (mm-40) REVERT: C 73 ASP cc_start: 0.7730 (t0) cc_final: 0.7160 (t0) REVERT: C 77 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8526 (p) REVERT: C 87 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7911 (ptp-110) REVERT: I 11 LEU cc_start: 0.8504 (tp) cc_final: 0.8268 (tt) REVERT: I 82 ASP cc_start: 0.8771 (m-30) cc_final: 0.8532 (m-30) outliers start: 55 outliers final: 12 residues processed: 244 average time/residue: 1.6804 time to fit residues: 454.4185 Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 6 GLN A 39 GLN D 6 GLN K 347 HIS K 441 ASN B 39 GLN H 6 GLN H 32 ASN H 92 ASN C 39 GLN I 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20756 Z= 0.225 Angle : 0.630 9.056 28182 Z= 0.318 Chirality : 0.045 0.186 3292 Planarity : 0.004 0.048 3534 Dihedral : 6.920 52.441 4264 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 2.94 % Allowed : 11.92 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.28 (0.16), residues: 2488 helix: -0.22 (1.05), residues: 24 sheet: 0.45 (0.16), residues: 1080 loop : -0.68 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 178 HIS 0.003 0.001 HIS K 184 PHE 0.013 0.002 PHE L 410 TYR 0.014 0.001 TYR K 121 ARG 0.011 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 2.316 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 10 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8779 (mp0) REVERT: E 23 LYS cc_start: 0.9128 (tttp) cc_final: 0.8820 (tttp) REVERT: E 39 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: E 65 GLN cc_start: 0.8600 (tt0) cc_final: 0.8142 (mm-40) REVERT: E 73 ASP cc_start: 0.7746 (t0) cc_final: 0.7161 (t0) REVERT: E 77 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 11 LEU cc_start: 0.8507 (tp) cc_final: 0.8296 (tt) REVERT: F 81 GLU cc_start: 0.9168 (mp0) cc_final: 0.8902 (pm20) REVERT: F 82 ASP cc_start: 0.8630 (m-30) cc_final: 0.8409 (m-30) REVERT: A 10 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8775 (tp30) REVERT: A 39 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: A 65 GLN cc_start: 0.8561 (tt0) cc_final: 0.8148 (mm-40) REVERT: A 73 ASP cc_start: 0.7751 (t0) cc_final: 0.7170 (t0) REVERT: D 11 LEU cc_start: 0.8514 (tp) cc_final: 0.8287 (tt) REVERT: D 81 GLU cc_start: 0.9088 (pm20) cc_final: 0.8816 (pm20) REVERT: D 82 ASP cc_start: 0.8744 (m-30) cc_final: 0.8068 (m-30) REVERT: B 10 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8790 (mp0) REVERT: B 23 LYS cc_start: 0.9128 (tttp) cc_final: 0.8822 (tttp) REVERT: B 39 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: B 65 GLN cc_start: 0.8594 (tt0) cc_final: 0.8128 (mm-40) REVERT: B 73 ASP cc_start: 0.7747 (t0) cc_final: 0.7157 (t0) REVERT: B 77 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 87 ARG cc_start: 0.8231 (ptp-110) cc_final: 0.7943 (ptp-170) REVERT: H 11 LEU cc_start: 0.8492 (tp) cc_final: 0.8262 (tt) REVERT: H 81 GLU cc_start: 0.9165 (mp0) cc_final: 0.8900 (pm20) REVERT: H 82 ASP cc_start: 0.8604 (m-30) cc_final: 0.8369 (m-30) REVERT: C 10 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8790 (mp0) REVERT: C 23 LYS cc_start: 0.9134 (tttp) cc_final: 0.8828 (tttp) REVERT: C 39 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: C 65 GLN cc_start: 0.8591 (tt0) cc_final: 0.8196 (mm-40) REVERT: C 73 ASP cc_start: 0.7746 (t0) cc_final: 0.7161 (t0) REVERT: C 77 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8511 (p) REVERT: I 11 LEU cc_start: 0.8499 (tp) cc_final: 0.8285 (tt) REVERT: I 82 ASP cc_start: 0.8654 (m-30) cc_final: 0.8247 (m-30) outliers start: 63 outliers final: 22 residues processed: 253 average time/residue: 1.7203 time to fit residues: 489.8012 Evaluate side-chains 236 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 6 GLN A 39 GLN D 6 GLN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN H 6 GLN L 441 ASN C 39 GLN I 6 GLN I 32 ASN I 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20756 Z= 0.246 Angle : 0.646 9.423 28182 Z= 0.324 Chirality : 0.045 0.188 3292 Planarity : 0.004 0.053 3534 Dihedral : 6.833 51.507 4264 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.22 % Rotamer: Outliers : 2.66 % Allowed : 12.71 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.36 (0.16), residues: 2488 helix: -0.25 (1.05), residues: 24 sheet: 0.38 (0.16), residues: 1068 loop : -0.72 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 178 HIS 0.004 0.001 HIS J 184 PHE 0.013 0.002 PHE L 410 TYR 0.019 0.001 TYR D 49 ARG 0.012 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 2.326 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 10 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8753 (mp0) REVERT: E 23 LYS cc_start: 0.9134 (tttp) cc_final: 0.8704 (tttp) REVERT: E 39 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 65 GLN cc_start: 0.8629 (tt0) cc_final: 0.8177 (mm-40) REVERT: E 73 ASP cc_start: 0.7764 (t0) cc_final: 0.7206 (t0) REVERT: E 77 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8416 (p) REVERT: F 6 GLN cc_start: 0.8235 (tt0) cc_final: 0.7880 (tt0) REVERT: F 11 LEU cc_start: 0.8505 (tp) cc_final: 0.8266 (tt) REVERT: F 81 GLU cc_start: 0.9214 (mp0) cc_final: 0.8913 (pm20) REVERT: F 82 ASP cc_start: 0.8632 (m-30) cc_final: 0.8397 (m-30) REVERT: A 10 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8717 (tp30) REVERT: A 65 GLN cc_start: 0.8612 (tt0) cc_final: 0.8113 (mm-40) REVERT: A 73 ASP cc_start: 0.7747 (t0) cc_final: 0.7200 (t0) REVERT: A 77 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8518 (p) REVERT: D 6 GLN cc_start: 0.8223 (tt0) cc_final: 0.7867 (tt0) REVERT: D 11 LEU cc_start: 0.8508 (tp) cc_final: 0.8268 (tt) REVERT: D 81 GLU cc_start: 0.9141 (pm20) cc_final: 0.8823 (pm20) REVERT: D 82 ASP cc_start: 0.8720 (m-30) cc_final: 0.8002 (m-30) REVERT: B 10 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8752 (mp0) REVERT: B 23 LYS cc_start: 0.9136 (tttp) cc_final: 0.8703 (tttp) REVERT: B 39 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 65 GLN cc_start: 0.8605 (tt0) cc_final: 0.8176 (mm-40) REVERT: B 73 ASP cc_start: 0.7765 (t0) cc_final: 0.7210 (t0) REVERT: B 77 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8427 (p) REVERT: B 87 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8242 (ptp-170) REVERT: H 6 GLN cc_start: 0.8221 (tt0) cc_final: 0.7866 (tt0) REVERT: H 11 LEU cc_start: 0.8504 (tp) cc_final: 0.8266 (tt) REVERT: H 81 GLU cc_start: 0.9212 (mp0) cc_final: 0.8912 (pm20) REVERT: H 82 ASP cc_start: 0.8628 (m-30) cc_final: 0.8394 (m-30) REVERT: C 10 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8753 (mp0) REVERT: C 23 LYS cc_start: 0.9142 (tttp) cc_final: 0.8711 (tttp) REVERT: C 39 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: C 65 GLN cc_start: 0.8622 (tt0) cc_final: 0.8151 (mm-40) REVERT: C 73 ASP cc_start: 0.7764 (t0) cc_final: 0.7204 (t0) REVERT: C 77 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8416 (p) REVERT: I 6 GLN cc_start: 0.8229 (tt0) cc_final: 0.7870 (tt0) REVERT: I 11 LEU cc_start: 0.8510 (tp) cc_final: 0.8280 (tt) REVERT: I 81 GLU cc_start: 0.9145 (mp0) cc_final: 0.8877 (pm20) REVERT: I 82 ASP cc_start: 0.8562 (m-30) cc_final: 0.8306 (m-30) outliers start: 57 outliers final: 27 residues processed: 250 average time/residue: 1.6990 time to fit residues: 470.7918 Evaluate side-chains 234 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 217 optimal weight: 0.3980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 441 ASN E 39 GLN F 32 ASN F 92 ASN J 441 ASN A 39 GLN D 32 ASN D 92 ASN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN C 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20756 Z= 0.188 Angle : 0.634 9.826 28182 Z= 0.315 Chirality : 0.045 0.186 3292 Planarity : 0.005 0.056 3534 Dihedral : 6.604 48.680 4264 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 2.90 % Allowed : 12.43 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.29 (0.16), residues: 2488 helix: -0.25 (1.03), residues: 24 sheet: 0.40 (0.16), residues: 1068 loop : -0.65 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 178 HIS 0.003 0.001 HIS J 184 PHE 0.012 0.002 PHE J 422 TYR 0.012 0.001 TYR K 121 ARG 0.013 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 2.543 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 10 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8791 (mp0) REVERT: E 23 LYS cc_start: 0.9129 (tttp) cc_final: 0.8697 (tttp) REVERT: E 39 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: E 65 GLN cc_start: 0.8604 (tt0) cc_final: 0.8165 (mm-40) REVERT: E 73 ASP cc_start: 0.7771 (t0) cc_final: 0.7202 (t0) REVERT: E 77 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8434 (p) REVERT: F 6 GLN cc_start: 0.8032 (tt0) cc_final: 0.7668 (tt0) REVERT: F 11 LEU cc_start: 0.8489 (tp) cc_final: 0.8267 (tt) REVERT: F 81 GLU cc_start: 0.9225 (mp0) cc_final: 0.8913 (pm20) REVERT: F 82 ASP cc_start: 0.8629 (m-30) cc_final: 0.8395 (m-30) REVERT: A 10 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8701 (tp30) REVERT: A 65 GLN cc_start: 0.8561 (tt0) cc_final: 0.8143 (mm-40) REVERT: A 73 ASP cc_start: 0.7729 (t0) cc_final: 0.7177 (t0) REVERT: D 6 GLN cc_start: 0.8022 (tt0) cc_final: 0.7648 (tt0) REVERT: D 11 LEU cc_start: 0.8494 (tp) cc_final: 0.8270 (tt) REVERT: D 81 GLU cc_start: 0.9136 (pm20) cc_final: 0.8824 (pm20) REVERT: D 82 ASP cc_start: 0.8766 (m-30) cc_final: 0.8161 (m-30) REVERT: B 10 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8788 (mp0) REVERT: B 23 LYS cc_start: 0.9131 (tttp) cc_final: 0.8703 (tttp) REVERT: B 39 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: B 65 GLN cc_start: 0.8605 (tt0) cc_final: 0.8169 (mm-40) REVERT: B 73 ASP cc_start: 0.7775 (t0) cc_final: 0.7182 (t0) REVERT: B 77 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (p) REVERT: B 87 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8317 (ptp-170) REVERT: H 6 GLN cc_start: 0.8024 (tt0) cc_final: 0.7662 (tt0) REVERT: H 11 LEU cc_start: 0.8492 (tp) cc_final: 0.8271 (tt) REVERT: H 81 GLU cc_start: 0.9218 (mp0) cc_final: 0.8912 (pm20) REVERT: H 82 ASP cc_start: 0.8620 (m-30) cc_final: 0.8387 (m-30) REVERT: C 10 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8790 (mp0) REVERT: C 23 LYS cc_start: 0.9137 (tttp) cc_final: 0.8711 (tttp) REVERT: C 39 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: C 65 GLN cc_start: 0.8590 (tt0) cc_final: 0.8142 (mm-40) REVERT: C 73 ASP cc_start: 0.7769 (t0) cc_final: 0.7202 (t0) REVERT: C 77 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8391 (p) REVERT: I 6 GLN cc_start: 0.8019 (tt0) cc_final: 0.7658 (tt0) REVERT: I 11 LEU cc_start: 0.8504 (tp) cc_final: 0.8281 (tt) REVERT: I 81 GLU cc_start: 0.9191 (mp0) cc_final: 0.8915 (pm20) REVERT: I 82 ASP cc_start: 0.8568 (m-30) cc_final: 0.8307 (m-30) outliers start: 62 outliers final: 29 residues processed: 261 average time/residue: 1.6526 time to fit residues: 478.7908 Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN A 39 GLN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20756 Z= 0.223 Angle : 0.654 9.951 28182 Z= 0.325 Chirality : 0.045 0.188 3292 Planarity : 0.005 0.059 3534 Dihedral : 6.555 48.260 4264 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.38 % Allowed : 13.36 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.33 (0.16), residues: 2488 helix: -0.26 (1.04), residues: 24 sheet: 0.39 (0.16), residues: 1068 loop : -0.69 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 178 HIS 0.003 0.001 HIS G 184 PHE 0.012 0.002 PHE G 422 TYR 0.022 0.001 TYR H 49 ARG 0.015 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 2.521 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 10 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8853 (mp0) REVERT: E 23 LYS cc_start: 0.9143 (tttp) cc_final: 0.8715 (tttp) REVERT: E 39 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: E 65 GLN cc_start: 0.8671 (tt0) cc_final: 0.8263 (mm-40) REVERT: E 73 ASP cc_start: 0.7734 (t0) cc_final: 0.7161 (t0) REVERT: E 77 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8487 (p) REVERT: F 6 GLN cc_start: 0.8215 (tt0) cc_final: 0.7956 (tt0) REVERT: F 11 LEU cc_start: 0.8492 (tp) cc_final: 0.8274 (tt) REVERT: F 81 GLU cc_start: 0.9253 (mp0) cc_final: 0.8945 (pm20) REVERT: F 82 ASP cc_start: 0.8627 (m-30) cc_final: 0.8380 (m-30) REVERT: A 10 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8735 (mp0) REVERT: A 12 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8863 (mmmm) REVERT: A 23 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8815 (tptp) REVERT: A 65 GLN cc_start: 0.8671 (tt0) cc_final: 0.8243 (mm-40) REVERT: A 73 ASP cc_start: 0.7765 (t0) cc_final: 0.7217 (t0) REVERT: D 3 VAL cc_start: 0.9267 (t) cc_final: 0.9045 (m) REVERT: D 6 GLN cc_start: 0.8168 (tt0) cc_final: 0.7905 (tt0) REVERT: D 11 LEU cc_start: 0.8496 (tp) cc_final: 0.8277 (tt) REVERT: D 79 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7799 (mp-120) REVERT: D 81 GLU cc_start: 0.9114 (pm20) cc_final: 0.8786 (pm20) REVERT: D 82 ASP cc_start: 0.8664 (m-30) cc_final: 0.7753 (m-30) REVERT: B 10 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8849 (mp0) REVERT: B 23 LYS cc_start: 0.9144 (tttp) cc_final: 0.8721 (tttp) REVERT: B 39 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: B 65 GLN cc_start: 0.8708 (tt0) cc_final: 0.8299 (mm-40) REVERT: B 73 ASP cc_start: 0.7735 (t0) cc_final: 0.7172 (t0) REVERT: B 77 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 87 ARG cc_start: 0.8500 (ptp-110) cc_final: 0.8246 (ptp-170) REVERT: H 3 VAL cc_start: 0.9269 (t) cc_final: 0.9052 (m) REVERT: H 6 GLN cc_start: 0.8173 (tt0) cc_final: 0.7907 (tt0) REVERT: H 11 LEU cc_start: 0.8498 (tp) cc_final: 0.8277 (tt) REVERT: H 81 GLU cc_start: 0.9252 (mp0) cc_final: 0.8944 (pm20) REVERT: H 82 ASP cc_start: 0.8618 (m-30) cc_final: 0.8373 (m-30) REVERT: C 10 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8853 (mp0) REVERT: C 23 LYS cc_start: 0.9149 (tttp) cc_final: 0.8726 (tttp) REVERT: C 39 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: C 65 GLN cc_start: 0.8622 (tt0) cc_final: 0.8221 (mm-40) REVERT: C 73 ASP cc_start: 0.7734 (t0) cc_final: 0.7160 (t0) REVERT: C 77 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8438 (p) REVERT: I 3 VAL cc_start: 0.9265 (t) cc_final: 0.9048 (m) REVERT: I 6 GLN cc_start: 0.8220 (tt0) cc_final: 0.7959 (tt0) REVERT: I 11 LEU cc_start: 0.8491 (tp) cc_final: 0.8278 (tt) REVERT: I 81 GLU cc_start: 0.9215 (mp0) cc_final: 0.8935 (pm20) REVERT: I 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8375 (m-30) outliers start: 51 outliers final: 32 residues processed: 254 average time/residue: 1.6313 time to fit residues: 462.0138 Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 chunk 163 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN A 39 GLN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20756 Z= 0.242 Angle : 0.663 9.940 28182 Z= 0.329 Chirality : 0.045 0.188 3292 Planarity : 0.005 0.061 3534 Dihedral : 6.528 48.165 4264 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 2.01 % Allowed : 13.74 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.35 (0.16), residues: 2488 helix: -0.25 (1.04), residues: 24 sheet: 0.35 (0.16), residues: 1076 loop : -0.68 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 178 HIS 0.004 0.001 HIS K 184 PHE 0.013 0.002 PHE L 410 TYR 0.014 0.001 TYR K 121 ARG 0.015 0.001 ARG F 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 2.648 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 10 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8853 (mp0) REVERT: E 23 LYS cc_start: 0.9152 (tttp) cc_final: 0.8726 (tttp) REVERT: E 39 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: E 65 GLN cc_start: 0.8653 (tt0) cc_final: 0.8254 (mm-40) REVERT: E 73 ASP cc_start: 0.7749 (t0) cc_final: 0.7176 (t0) REVERT: E 77 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8542 (p) REVERT: F 3 VAL cc_start: 0.9276 (t) cc_final: 0.9029 (m) REVERT: F 6 GLN cc_start: 0.8113 (tt0) cc_final: 0.7859 (tt0) REVERT: F 11 LEU cc_start: 0.8490 (tp) cc_final: 0.8276 (tt) REVERT: F 81 GLU cc_start: 0.9282 (mp0) cc_final: 0.8975 (pm20) REVERT: F 82 ASP cc_start: 0.8672 (m-30) cc_final: 0.8415 (m-30) REVERT: A 10 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8744 (mp0) REVERT: A 12 LYS cc_start: 0.9187 (mmtp) cc_final: 0.8877 (mmmm) REVERT: A 65 GLN cc_start: 0.8648 (tt0) cc_final: 0.8296 (mm-40) REVERT: A 73 ASP cc_start: 0.7830 (t0) cc_final: 0.7303 (t0) REVERT: D 3 VAL cc_start: 0.9270 (t) cc_final: 0.9023 (m) REVERT: D 6 GLN cc_start: 0.8111 (tt0) cc_final: 0.7882 (tt0) REVERT: D 11 LEU cc_start: 0.8496 (tp) cc_final: 0.8282 (tt) REVERT: D 81 GLU cc_start: 0.9109 (pm20) cc_final: 0.8791 (pm20) REVERT: D 82 ASP cc_start: 0.8622 (m-30) cc_final: 0.8036 (m-30) REVERT: B 10 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8852 (mp0) REVERT: B 23 LYS cc_start: 0.9149 (tttp) cc_final: 0.8727 (tttp) REVERT: B 39 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: B 65 GLN cc_start: 0.8676 (tt0) cc_final: 0.8285 (mm-40) REVERT: B 73 ASP cc_start: 0.7750 (t0) cc_final: 0.7187 (t0) REVERT: B 77 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 87 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.8221 (ptp-170) REVERT: H 3 VAL cc_start: 0.9278 (t) cc_final: 0.9036 (m) REVERT: H 6 GLN cc_start: 0.8117 (tt0) cc_final: 0.7883 (tt0) REVERT: H 11 LEU cc_start: 0.8496 (tp) cc_final: 0.8280 (tt) REVERT: H 81 GLU cc_start: 0.9281 (mp0) cc_final: 0.8974 (pm20) REVERT: H 82 ASP cc_start: 0.8660 (m-30) cc_final: 0.8407 (m-30) REVERT: C 10 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8854 (mp0) REVERT: C 23 LYS cc_start: 0.9156 (tttp) cc_final: 0.8733 (tttp) REVERT: C 39 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: C 65 GLN cc_start: 0.8640 (tt0) cc_final: 0.8207 (mm-40) REVERT: C 73 ASP cc_start: 0.7748 (t0) cc_final: 0.7176 (t0) REVERT: C 77 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 87 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7888 (ptp-170) REVERT: I 3 VAL cc_start: 0.9277 (t) cc_final: 0.9034 (m) REVERT: I 6 GLN cc_start: 0.8125 (tt0) cc_final: 0.7888 (tt0) REVERT: I 11 LEU cc_start: 0.8488 (tp) cc_final: 0.8278 (tt) REVERT: I 81 GLU cc_start: 0.9210 (mp0) cc_final: 0.8922 (pm20) REVERT: I 82 ASP cc_start: 0.8647 (m-30) cc_final: 0.8345 (m-30) outliers start: 43 outliers final: 32 residues processed: 253 average time/residue: 1.7043 time to fit residues: 479.2099 Evaluate side-chains 258 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 467 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 467 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain I residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059088 restraints weight = 39824.221| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.92 r_work: 0.2766 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20756 Z= 0.206 Angle : 0.656 10.117 28182 Z= 0.324 Chirality : 0.045 0.188 3292 Planarity : 0.005 0.060 3534 Dihedral : 6.376 46.333 4264 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % Rotamer: Outliers : 2.20 % Allowed : 13.64 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.17 % 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: -0.31 (0.16), residues: 2488 helix: -0.26 (1.03), residues: 24 sheet: 0.41 (0.16), residues: 1076 loop : -0.68 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 178 HIS 0.003 0.001 HIS G 184 PHE 0.012 0.002 PHE G 422 TYR 0.023 0.001 TYR F 49 ARG 0.014 0.001 ARG D 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8270.71 seconds wall clock time: 150 minutes 4.51 seconds (9004.51 seconds total)