Starting phenix.real_space_refine on Tue Nov 19 05:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3q_29708/11_2024/8g3q_29708.cif" } resolution = 2.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11520 2.51 5 N 3120 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 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: 18618 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" 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: "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: "H" 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: "F" 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "D" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "a" 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: "b" 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: "c" 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: "d" 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: "f" 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: "g" 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: "i" 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: "j" 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: "k" 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: "l" 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 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: 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: "v" 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: "w" 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: "1" 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: "2" 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: "3" 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: "4" 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: "6" 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: "7" 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: "E" 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" 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: 11.98, per 1000 atoms: 0.64 Number of scatterers: 18618 At special positions: 0 Unit cell: (134.48, 136.12, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3864 8.00 N 3120 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.98 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.08 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.05 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.04 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.07 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.16 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=2.06 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.01 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.07 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.06 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.07 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.04 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.12 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=1.99 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.06 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.07 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.08 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.05 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.06 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.07 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=1.99 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.06 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.07 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.07 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.04 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS F 337 " distance=2.08 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 447 " distance=2.14 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 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 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " NAG-ASN " NAG 1 1 " - " ASN H 86 " " NAG 2 1 " - " ASN H 146 " " NAG 3 1 " - " ASN H 200 " " NAG 4 1 " - " ASN H 234 " " NAG 6 1 " - " ASN H 329 " " NAG 7 1 " - " ASN H 367 " " NAG a 1 " - " ASN E 86 " " NAG b 1 " - " ASN E 146 " " NAG c 1 " - " ASN E 200 " " NAG d 1 " - " ASN E 234 " " NAG f 1 " - " ASN E 329 " " NAG g 1 " - " ASN E 367 " " NAG i 1 " - " ASN F 86 " " NAG j 1 " - " ASN F 146 " " NAG k 1 " - " ASN F 200 " " NAG l 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 329 " " NAG o 1 " - " ASN F 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: 6.04 Conformation dependent library (CDL) restraints added in 2.4 seconds 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4098 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 42 sheets defined 3.4% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.747A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.835A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.668A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.673A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.021A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.466A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.288A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.381A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.313A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.432A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.071A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.680A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.676A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.040A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.467A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.289A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.384A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.498A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.696A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.674A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.012A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.461A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.308A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.389A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.330A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.441A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.675A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG F 420 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.667A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 172 " --> pdb=" O MET F 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 184 removed outlier: 3.993A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 207 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU F 211 " --> pdb=" O TYR F 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 6.455A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 283 removed outlier: 5.285A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 352 through 356 removed outlier: 4.419A pdb=" N TRP F 352 " --> pdb=" O GLY F 363 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.316A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.484A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.500A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.492A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASN C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.475A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.575A pdb=" N ASN I 117 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.509A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.505A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.550A pdb=" N ASN A 117 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 104 through 105 613 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3243 1.31 - 1.44: 5080 1.44 - 1.57: 10556 1.57 - 1.69: 0 1.69 - 1.82: 134 Bond restraints: 19013 Sorted by residual: bond pdb=" N GLY F 286 " pdb=" CA GLY F 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.73e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.69e-02 3.50e+03 1.73e+01 bond pdb=" C SER H 88 " pdb=" O SER H 88 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.26e-02 6.30e+03 1.70e+01 bond pdb=" CA SER H 384 " pdb=" CB SER H 384 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.45e-02 4.76e+03 1.69e+01 bond pdb=" C PRO H 166 " pdb=" O PRO H 166 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.18e-02 7.18e+03 1.67e+01 ... (remaining 19008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 23579 2.95 - 5.90: 2142 5.90 - 8.84: 82 8.84 - 11.79: 3 11.79 - 14.74: 3 Bond angle restraints: 25809 Sorted by residual: angle pdb=" CG ARG A 106 " pdb=" CD ARG A 106 " pdb=" NE ARG A 106 " ideal model delta sigma weight residual 112.00 126.74 -14.74 2.20e+00 2.07e-01 4.49e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.81 106.10 5.71 8.60e-01 1.35e+00 4.40e+01 angle pdb=" OD1 ASN H 294 " pdb=" CG ASN H 294 " pdb=" ND2 ASN H 294 " ideal model delta sigma weight residual 122.60 129.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CG ARG I 106 " pdb=" CD ARG I 106 " pdb=" NE ARG I 106 " ideal model delta sigma weight residual 112.00 126.39 -14.39 2.20e+00 2.07e-01 4.28e+01 angle pdb=" CG ARG C 106 " pdb=" CD ARG C 106 " pdb=" NE ARG C 106 " ideal model delta sigma weight residual 112.00 126.32 -14.32 2.20e+00 2.07e-01 4.24e+01 ... (remaining 25804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 11606 22.49 - 44.98: 525 44.98 - 67.46: 97 67.46 - 89.95: 132 89.95 - 112.44: 90 Dihedral angle restraints: 12450 sinusoidal: 6015 harmonic: 6435 Sorted by residual: dihedral pdb=" CA ALA C 9 " pdb=" C ALA C 9 " pdb=" N GLU C 10 " pdb=" CA GLU C 10 " ideal model delta harmonic sigma weight residual 180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY B 57 " pdb=" C GLY B 57 " pdb=" N VAL B 58 " pdb=" CA VAL B 58 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" N CYS A 96 " pdb=" CA CYS A 96 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 12447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1659 0.069 - 0.138: 1029 0.138 - 0.208: 328 0.208 - 0.277: 62 0.277 - 0.346: 7 Chirality restraints: 3085 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.82e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.84e+01 chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.54e+01 ... (remaining 3082 not shown) Planarity restraints: 3215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.079 2.00e-02 2.50e+03 4.26e-02 3.62e+01 pdb=" CG TYR E 281 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 281 " -0.080 2.00e-02 2.50e+03 4.16e-02 3.46e+01 pdb=" CG TYR F 281 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR F 281 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR F 281 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR F 281 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 281 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 281 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 281 " -0.076 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR H 281 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR H 281 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR H 281 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR H 281 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 281 " -0.056 2.00e-02 2.50e+03 ... (remaining 3212 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2089 2.76 - 3.29: 18605 3.29 - 3.83: 34654 3.83 - 4.36: 45039 4.36 - 4.90: 71580 Nonbonded interactions: 171967 Sorted by model distance: nonbonded pdb=" O ASP H 293 " pdb="CA CA H2000 " model vdw 2.222 2.510 nonbonded pdb=" OD2 ASP F 324 " pdb="CA CA F2000 " model vdw 2.233 2.510 nonbonded pdb=" O ASP G 293 " pdb="CA CA G2000 " model vdw 2.251 2.510 nonbonded pdb=" O GLY H 345 " pdb="CA CA H2000 " model vdw 2.257 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.257 2.510 ... (remaining 171962 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 '1' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and (resid 82 through 469 or resid 501)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 45.280 Find NCS groups from input model: 1.000 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 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 : 0.014 0.070 19013 Z= 0.921 Angle : 1.705 14.740 25809 Z= 1.085 Chirality : 0.092 0.346 3085 Planarity : 0.011 0.079 3191 Dihedral : 18.860 112.437 8226 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.16 % Favored : 96.44 % Rotamer: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2246 helix: -1.22 (0.94), residues: 24 sheet: -0.26 (0.16), residues: 885 loop : -0.83 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.014 TRP H 178 HIS 0.019 0.006 HIS H 336 PHE 0.049 0.012 PHE E 446 TYR 0.080 0.015 TYR F 281 ARG 0.036 0.003 ARG H 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 178 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.9173 (p-90) REVERT: H 150 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8210 (tpt90) REVERT: F 178 TRP cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (p-90) REVERT: B 17 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8525 (mm-30) REVERT: C 10 GLU cc_start: 0.8802 (tp30) cc_final: 0.8220 (tp30) REVERT: C 43 GLN cc_start: 0.8894 (mt0) cc_final: 0.8569 (mm-40) REVERT: D 59 PRO cc_start: 0.9517 (Cg_exo) cc_final: 0.9139 (Cg_endo) REVERT: L 2 ILE cc_start: 0.8154 (mt) cc_final: 0.7948 (mt) REVERT: L 17 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8750 (mp0) REVERT: L 54 ARG cc_start: 0.9238 (mtm-85) cc_final: 0.8954 (mtm-85) REVERT: L 81 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8738 (mt-10) REVERT: L 98 THR cc_start: 0.9194 (m) cc_final: 0.8726 (p) REVERT: A 23 LYS cc_start: 0.8942 (tttt) cc_final: 0.8668 (tttp) REVERT: A 81 MET cc_start: 0.9229 (ttp) cc_final: 0.9028 (ttp) outliers start: 4 outliers final: 0 residues processed: 273 average time/residue: 1.6774 time to fit residues: 506.5709 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain F residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 HIS E 465 ASN G 147 ASN H 147 ASN B 6 GLN C 32 ASN D 27 GLN A 31 ASN A 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19013 Z= 0.276 Angle : 0.726 6.447 25809 Z= 0.373 Chirality : 0.049 0.173 3085 Planarity : 0.004 0.041 3191 Dihedral : 14.486 80.081 4293 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 0.98 % Allowed : 7.27 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2246 helix: -1.16 (0.57), residues: 24 sheet: -0.09 (0.18), residues: 813 loop : -0.23 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 178 HIS 0.003 0.001 HIS G 168 PHE 0.017 0.002 PHE G 410 TYR 0.019 0.002 TYR L 91 ARG 0.008 0.001 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8525 (mm-30) REVERT: B 59 PRO cc_start: 0.9510 (Cg_exo) cc_final: 0.9293 (Cg_endo) REVERT: B 81 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8875 (tm-30) REVERT: B 82 ASP cc_start: 0.9202 (m-30) cc_final: 0.8968 (m-30) REVERT: C 43 GLN cc_start: 0.8864 (mt0) cc_final: 0.8581 (mm-40) REVERT: D 59 PRO cc_start: 0.9487 (Cg_exo) cc_final: 0.9187 (Cg_endo) REVERT: I 3 GLN cc_start: 0.8932 (tt0) cc_final: 0.8675 (tp-100) REVERT: I 43 GLN cc_start: 0.7853 (mt0) cc_final: 0.7204 (mp10) REVERT: L 17 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8779 (mp0) REVERT: L 54 ARG cc_start: 0.9218 (mtm-85) cc_final: 0.8851 (mtm-85) REVERT: L 81 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8911 (mt-10) REVERT: L 98 THR cc_start: 0.9244 (m) cc_final: 0.8873 (p) outliers start: 19 outliers final: 3 residues processed: 247 average time/residue: 1.6780 time to fit residues: 458.6503 Evaluate side-chains 228 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 176 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 159 optimal weight: 0.9980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN F 141 ASN B 6 GLN D 27 GLN I 31 ASN A 62 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19013 Z= 0.255 Angle : 0.666 6.361 25809 Z= 0.337 Chirality : 0.049 0.174 3085 Planarity : 0.004 0.053 3191 Dihedral : 10.388 64.718 4289 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 0.98 % Allowed : 8.56 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2246 helix: -1.04 (0.82), residues: 28 sheet: -0.12 (0.18), residues: 810 loop : 0.03 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 178 HIS 0.012 0.001 HIS H 336 PHE 0.017 0.002 PHE G 410 TYR 0.019 0.002 TYR E 121 ARG 0.013 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8651 (mm-30) REVERT: B 81 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8702 (tm-30) REVERT: B 82 ASP cc_start: 0.9260 (m-30) cc_final: 0.9006 (m-30) REVERT: B 107 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9193 (mt) REVERT: C 43 GLN cc_start: 0.8835 (mt0) cc_final: 0.8524 (mm-40) REVERT: D 59 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.9208 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7677 (ptm160) cc_final: 0.6486 (pmt170) REVERT: I 3 GLN cc_start: 0.8897 (tt0) cc_final: 0.8687 (tp-100) REVERT: I 43 GLN cc_start: 0.7907 (mt0) cc_final: 0.7288 (mp10) REVERT: L 17 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8795 (mp0) REVERT: L 54 ARG cc_start: 0.9193 (mtm-85) cc_final: 0.8836 (mtm-85) REVERT: L 81 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8867 (mp0) REVERT: L 98 THR cc_start: 0.9293 (m) cc_final: 0.9061 (p) REVERT: L 108 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8820 (ttpp) REVERT: A 43 GLN cc_start: 0.8330 (mp10) cc_final: 0.7632 (mp10) outliers start: 19 outliers final: 5 residues processed: 249 average time/residue: 1.6904 time to fit residues: 463.8563 Evaluate side-chains 232 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN G 347 HIS H 465 ASN F 141 ASN F 147 ASN B 27 GLN B 93 ASN A 32 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 19013 Z= 0.475 Angle : 0.691 6.083 25809 Z= 0.356 Chirality : 0.049 0.210 3085 Planarity : 0.004 0.047 3191 Dihedral : 8.877 68.547 4289 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 9.33 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2246 helix: 0.07 (0.90), residues: 24 sheet: -0.28 (0.17), residues: 847 loop : -0.03 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 178 HIS 0.005 0.001 HIS G 168 PHE 0.021 0.003 PHE G 410 TYR 0.021 0.002 TYR D 91 ARG 0.010 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8547 (mtp85) REVERT: H 467 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7612 (ptp) REVERT: B 17 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8660 (mm-30) REVERT: B 81 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8717 (tm-30) REVERT: B 107 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9153 (mt) REVERT: C 12 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8698 (mtpt) REVERT: C 43 GLN cc_start: 0.8899 (mt0) cc_final: 0.8607 (mm-40) REVERT: D 109 ARG cc_start: 0.7527 (ptm160) cc_final: 0.6524 (pmt170) REVERT: I 43 GLN cc_start: 0.7932 (mt0) cc_final: 0.7314 (mp10) REVERT: L 54 ARG cc_start: 0.9235 (mtm-85) cc_final: 0.8881 (mtm-85) REVERT: L 81 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8863 (mp0) REVERT: L 98 THR cc_start: 0.9340 (m) cc_final: 0.9125 (p) REVERT: A 43 GLN cc_start: 0.8341 (mp10) cc_final: 0.7684 (mp10) outliers start: 24 outliers final: 7 residues processed: 233 average time/residue: 1.5875 time to fit residues: 407.2566 Evaluate side-chains 225 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 189 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN C 117 ASN I 3 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19013 Z= 0.215 Angle : 0.602 5.585 25809 Z= 0.311 Chirality : 0.046 0.185 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.661 58.442 4289 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Rotamer: Outliers : 1.13 % Allowed : 10.36 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2246 helix: -0.81 (0.84), residues: 28 sheet: -0.26 (0.17), residues: 847 loop : 0.09 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 178 HIS 0.003 0.001 HIS H 274 PHE 0.016 0.002 PHE F 410 TYR 0.017 0.002 TYR D 91 ARG 0.006 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8849 (mtp-110) cc_final: 0.8377 (mmp-170) REVERT: B 17 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8672 (mm-30) REVERT: B 81 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8701 (tm-30) REVERT: C 43 GLN cc_start: 0.8899 (mt0) cc_final: 0.8562 (mm-40) REVERT: D 59 PRO cc_start: 0.9429 (Cg_exo) cc_final: 0.9143 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7500 (ptm160) cc_final: 0.6460 (pmt170) REVERT: I 43 GLN cc_start: 0.7960 (mt0) cc_final: 0.7471 (mp10) REVERT: I 73 ASP cc_start: 0.8563 (m-30) cc_final: 0.8328 (t0) REVERT: L 17 GLU cc_start: 0.8448 (mp0) cc_final: 0.7871 (mp0) REVERT: L 54 ARG cc_start: 0.9188 (mtm-85) cc_final: 0.8863 (mtm-85) REVERT: L 81 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8903 (mp0) REVERT: A 43 GLN cc_start: 0.8359 (mp10) cc_final: 0.7726 (mp10) outliers start: 22 outliers final: 6 residues processed: 245 average time/residue: 1.6151 time to fit residues: 437.3779 Evaluate side-chains 219 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 41 optimal weight: 0.0970 chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN F 141 ASN B 93 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19013 Z= 0.262 Angle : 0.600 5.782 25809 Z= 0.310 Chirality : 0.045 0.206 3085 Planarity : 0.004 0.042 3191 Dihedral : 7.455 57.531 4289 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 1.13 % Allowed : 11.39 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2246 helix: -0.72 (0.84), residues: 28 sheet: -0.24 (0.17), residues: 847 loop : 0.12 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 144 PHE 0.016 0.002 PHE G 410 TYR 0.023 0.002 TYR L 91 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8785 (mtp-110) cc_final: 0.8345 (mmp-170) REVERT: B 17 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8667 (mm-30) REVERT: B 81 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8711 (tm-30) REVERT: C 12 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8894 (mtpt) REVERT: C 43 GLN cc_start: 0.8902 (mt0) cc_final: 0.8549 (mm-40) REVERT: D 17 GLU cc_start: 0.8352 (mp0) cc_final: 0.8098 (mp0) REVERT: D 33 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9006 (tm) REVERT: I 38 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8008 (ptt180) REVERT: I 43 GLN cc_start: 0.7929 (mt0) cc_final: 0.7471 (mp10) REVERT: I 73 ASP cc_start: 0.8605 (m-30) cc_final: 0.8368 (t0) REVERT: L 17 GLU cc_start: 0.8427 (mp0) cc_final: 0.7931 (mp0) REVERT: L 54 ARG cc_start: 0.9178 (mtm-85) cc_final: 0.8856 (mtm-85) REVERT: L 81 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8912 (mp0) REVERT: A 23 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8727 (mtpp) REVERT: A 43 GLN cc_start: 0.8324 (mp10) cc_final: 0.7759 (mp10) outliers start: 22 outliers final: 7 residues processed: 224 average time/residue: 1.7074 time to fit residues: 420.8987 Evaluate side-chains 220 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 97 optimal weight: 0.0270 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19013 Z= 0.277 Angle : 0.599 6.416 25809 Z= 0.310 Chirality : 0.046 0.209 3085 Planarity : 0.004 0.044 3191 Dihedral : 7.334 56.544 4289 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.82 % Allowed : 11.86 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2246 helix: -0.66 (0.85), residues: 28 sheet: -0.26 (0.17), residues: 847 loop : 0.14 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 144 PHE 0.016 0.002 PHE G 410 TYR 0.022 0.002 TYR L 91 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8699 (mm-30) REVERT: B 81 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8604 (tm-30) REVERT: C 43 GLN cc_start: 0.8825 (mt0) cc_final: 0.8487 (mm-40) REVERT: C 78 THR cc_start: 0.9129 (m) cc_final: 0.8527 (p) REVERT: D 17 GLU cc_start: 0.8437 (mp0) cc_final: 0.8137 (mp0) REVERT: D 33 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8937 (tm) REVERT: I 38 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7986 (ptt180) REVERT: I 43 GLN cc_start: 0.7928 (mt0) cc_final: 0.7494 (mp10) REVERT: I 73 ASP cc_start: 0.8620 (m-30) cc_final: 0.8366 (t0) REVERT: I 117 ASN cc_start: 0.8881 (m110) cc_final: 0.8547 (m-40) REVERT: L 17 GLU cc_start: 0.8427 (mp0) cc_final: 0.7907 (mp0) REVERT: L 54 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8860 (mtm-85) REVERT: L 81 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8919 (mp0) REVERT: A 23 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8733 (mtpp) REVERT: A 43 GLN cc_start: 0.8322 (mp10) cc_final: 0.7909 (mp10) outliers start: 16 outliers final: 4 residues processed: 225 average time/residue: 1.6564 time to fit residues: 411.5550 Evaluate side-chains 217 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN H 465 ASN B 93 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19013 Z= 0.195 Angle : 0.578 6.600 25809 Z= 0.299 Chirality : 0.045 0.205 3085 Planarity : 0.004 0.046 3191 Dihedral : 6.969 59.190 4289 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 0.72 % Allowed : 12.84 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2246 helix: -0.69 (0.85), residues: 28 sheet: -0.36 (0.18), residues: 839 loop : 0.28 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS E 184 PHE 0.015 0.002 PHE F 410 TYR 0.018 0.002 TYR L 91 ARG 0.012 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 381 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8816 (mt-10) REVERT: B 17 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8727 (mm-30) REVERT: B 81 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8571 (tm-30) REVERT: C 43 GLN cc_start: 0.8811 (mt0) cc_final: 0.8473 (mm-40) REVERT: D 17 GLU cc_start: 0.8443 (mp0) cc_final: 0.8163 (mp0) REVERT: D 33 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8867 (tm) REVERT: I 43 GLN cc_start: 0.7868 (mt0) cc_final: 0.7434 (mp10) REVERT: I 73 ASP cc_start: 0.8633 (m-30) cc_final: 0.8389 (t0) REVERT: L 17 GLU cc_start: 0.8415 (mp0) cc_final: 0.7805 (mp0) REVERT: L 54 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.8830 (mtm-85) REVERT: L 81 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8922 (mp0) REVERT: A 13 ARG cc_start: 0.9217 (mmm-85) cc_final: 0.8675 (mtt-85) REVERT: A 23 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8758 (mtpp) REVERT: A 43 GLN cc_start: 0.8307 (mp10) cc_final: 0.7897 (mp10) outliers start: 14 outliers final: 3 residues processed: 232 average time/residue: 1.6575 time to fit residues: 424.2569 Evaluate side-chains 215 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.2980 chunk 201 optimal weight: 0.8980 chunk 183 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN F 141 ASN A 32 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19013 Z= 0.261 Angle : 0.592 6.720 25809 Z= 0.307 Chirality : 0.045 0.216 3085 Planarity : 0.004 0.064 3191 Dihedral : 7.001 55.958 4289 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.85 % Favored : 96.97 % Rotamer: Outliers : 0.82 % Allowed : 12.84 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2246 helix: -0.56 (0.87), residues: 28 sheet: -0.35 (0.18), residues: 839 loop : 0.28 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 118 HIS 0.003 0.001 HIS F 144 PHE 0.016 0.002 PHE D 83 TYR 0.020 0.002 TYR L 91 ARG 0.015 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 381 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8815 (mt-10) REVERT: B 17 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8710 (mm-30) REVERT: B 54 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8567 (mtm-85) REVERT: B 81 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8543 (tm-30) REVERT: B 107 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9084 (mt) REVERT: C 10 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8420 (mm-30) REVERT: C 43 GLN cc_start: 0.8837 (mt0) cc_final: 0.8480 (mm-40) REVERT: D 17 GLU cc_start: 0.8417 (mp0) cc_final: 0.8106 (mp0) REVERT: D 33 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8904 (tm) REVERT: I 38 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8464 (ptt180) REVERT: I 43 GLN cc_start: 0.7900 (mt0) cc_final: 0.7486 (mp10) REVERT: I 73 ASP cc_start: 0.8660 (m-30) cc_final: 0.8415 (t0) REVERT: L 17 GLU cc_start: 0.8431 (mp0) cc_final: 0.7998 (mp0) REVERT: L 54 ARG cc_start: 0.9106 (mtm-85) cc_final: 0.8838 (mtm-85) REVERT: L 81 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8947 (mp0) REVERT: A 13 ARG cc_start: 0.9250 (mmm-85) cc_final: 0.8766 (mtp85) REVERT: A 23 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8748 (mtpp) REVERT: A 43 GLN cc_start: 0.8299 (mp10) cc_final: 0.7935 (mp10) outliers start: 16 outliers final: 6 residues processed: 220 average time/residue: 1.6703 time to fit residues: 405.3426 Evaluate side-chains 222 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 217 optimal weight: 0.4980 chunk 199 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 0.0010 chunk 106 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN B 93 ASN A 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19013 Z= 0.175 Angle : 0.588 8.042 25809 Z= 0.305 Chirality : 0.045 0.208 3085 Planarity : 0.004 0.049 3191 Dihedral : 6.856 54.033 4289 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.57 % Allowed : 13.45 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2246 helix: -0.67 (0.83), residues: 28 sheet: -0.35 (0.18), residues: 839 loop : 0.31 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 PHE 0.016 0.002 PHE D 83 TYR 0.020 0.002 TYR L 91 ARG 0.014 0.001 ARG H 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 381 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8804 (mt-10) REVERT: B 17 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8707 (mm-30) REVERT: B 107 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9076 (mt) REVERT: C 10 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: C 43 GLN cc_start: 0.8843 (mt0) cc_final: 0.8477 (mm-40) REVERT: D 17 GLU cc_start: 0.8415 (mp0) cc_final: 0.8100 (mp0) REVERT: D 33 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8862 (tm) REVERT: I 38 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8441 (ptt180) REVERT: I 43 GLN cc_start: 0.7920 (mt0) cc_final: 0.7507 (mp10) REVERT: I 73 ASP cc_start: 0.8608 (m-30) cc_final: 0.8345 (t0) REVERT: L 17 GLU cc_start: 0.8418 (mp0) cc_final: 0.7982 (mp0) REVERT: L 54 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.8819 (mtm-85) REVERT: L 81 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8948 (mp0) REVERT: A 13 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8749 (mtp85) REVERT: A 23 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8768 (mtpp) REVERT: A 43 GLN cc_start: 0.8289 (mp10) cc_final: 0.7931 (mp10) REVERT: A 73 ASP cc_start: 0.8752 (t70) cc_final: 0.7890 (t0) outliers start: 11 outliers final: 4 residues processed: 222 average time/residue: 1.6919 time to fit residues: 413.8074 Evaluate side-chains 215 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 465 ASN F 141 ASN A 32 ASN A 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.058406 restraints weight = 31537.335| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.44 r_work: 0.2645 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19013 Z= 0.250 Angle : 0.592 7.719 25809 Z= 0.306 Chirality : 0.045 0.216 3085 Planarity : 0.004 0.067 3191 Dihedral : 6.853 51.285 4289 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 0.67 % Allowed : 13.35 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2246 helix: -0.57 (0.86), residues: 28 sheet: -0.34 (0.18), residues: 839 loop : 0.31 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS H 336 PHE 0.015 0.002 PHE F 410 TYR 0.020 0.002 TYR L 91 ARG 0.016 0.001 ARG H 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7622.17 seconds wall clock time: 149 minutes 29.83 seconds (8969.83 seconds total)