Starting phenix.real_space_refine on Mon Feb 19 13:47:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si5_40499/02_2024/8si5_40499_neut_trim_updated.pdb" } resolution = 2.17 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= 0.009 sd= 0.085 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 52 5.49 5 S 232 5.16 5 C 25580 2.51 5 N 5968 2.21 5 O 7116 1.98 5 H 35916 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 660": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 660": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 660": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 660": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74865 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 17843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 17843 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1052} Chain breaks: 3 Chain: "B" Number of atoms: 17843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 17843 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1052} Chain breaks: 3 Chain: "C" Number of atoms: 17843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 17843 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1052} Chain breaks: 3 Chain: "D" Number of atoms: 17843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 17843 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1052} Chain breaks: 3 Chain: "A" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 914 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 2, 'POV': 15, 'ZY8': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 720 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 12, 'ZY8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 735 Unusual residues: {'CLR': 1, 'POV': 13, 'ZY8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 720 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 12, 'ZY8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Time building chain proxies: 23.84, per 1000 atoms: 0.32 Number of scatterers: 74865 At special positions: 0 Unit cell: (183.43, 183.43, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 232 16.00 P 52 15.00 O 7116 8.00 N 5968 7.00 C 25580 6.00 H 35916 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.05 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.05 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.05 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 47.40 Conformation dependent library (CDL) restraints added in 5.7 seconds 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 12 sheets defined 56.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.02 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.812A pdb=" N LEU A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 58' Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.620A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 4.049A pdb=" N LEU A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.663A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.533A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.794A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 4.117A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.645A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.580A pdb=" N PHE A 490 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 493 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 621 through 631 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 648 through 667 Processing helix chain 'A' and resid 675 through 700 Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.544A pdb=" N PHE A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 Processing helix chain 'A' and resid 884 through 905 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 923 through 944 Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.591A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1001 through 1022 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1031 through 1045 removed outlier: 3.645A pdb=" N VAL A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N HIS A1039 " --> pdb=" O ASP A1035 " (cutoff:3.500A) Proline residue: A1040 - end of helix removed outlier: 3.735A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1070 through 1085 Proline residue: A1074 - end of helix removed outlier: 3.808A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1124 removed outlier: 3.750A pdb=" N ILE A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1145 removed outlier: 4.129A pdb=" N PHE A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS A1143 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1191 Processing helix chain 'A' and resid 1193 through 1228 removed outlier: 3.524A pdb=" N ILE A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A1220 " --> pdb=" O ASP A1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 35 through 38 No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.812A pdb=" N LEU B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 58' Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.621A pdb=" N ARG B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 4.049A pdb=" N LEU B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.663A pdb=" N LYS B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.533A pdb=" N THR B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 371 removed outlier: 3.795A pdb=" N MET B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 4.117A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.645A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 471 through 478 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.581A pdb=" N PHE B 490 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 493 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 648 through 667 Processing helix chain 'B' and resid 675 through 700 Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 737 through 748 Processing helix chain 'B' and resid 757 through 766 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.544A pdb=" N PHE B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 Processing helix chain 'B' and resid 884 through 905 Processing helix chain 'B' and resid 912 through 921 Processing helix chain 'B' and resid 923 through 944 Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.590A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 Processing helix chain 'B' and resid 1001 through 1022 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1031 through 1045 removed outlier: 3.644A pdb=" N VAL B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS B1039 " --> pdb=" O ASP B1035 " (cutoff:3.500A) Proline residue: B1040 - end of helix removed outlier: 3.736A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1052 No H-bonds generated for 'chain 'B' and resid 1050 through 1052' Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1070 through 1085 Proline residue: B1074 - end of helix removed outlier: 3.808A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1124 removed outlier: 3.750A pdb=" N ILE B1106 " --> pdb=" O GLN B1102 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1145 removed outlier: 4.129A pdb=" N PHE B1142 " --> pdb=" O ILE B1138 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1191 Processing helix chain 'B' and resid 1193 through 1228 removed outlier: 3.524A pdb=" N ILE B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B1220 " --> pdb=" O ASP B1216 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.811A pdb=" N LEU C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 58' Processing helix chain 'C' and resid 72 through 75 No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.620A pdb=" N ARG C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.049A pdb=" N LEU C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.663A pdb=" N LYS C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.533A pdb=" N THR C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.795A pdb=" N MET C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 removed outlier: 4.117A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 417 removed outlier: 3.645A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 452 through 460 Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.581A pdb=" N PHE C 490 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 493 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 531 through 537 Processing helix chain 'C' and resid 621 through 631 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 648 through 667 Processing helix chain 'C' and resid 675 through 700 Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 757 through 766 Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.544A pdb=" N PHE C 845 " --> pdb=" O ILE C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 Processing helix chain 'C' and resid 884 through 905 Processing helix chain 'C' and resid 912 through 921 Processing helix chain 'C' and resid 923 through 944 Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.590A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 999 Processing helix chain 'C' and resid 1001 through 1022 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1031 through 1045 removed outlier: 3.645A pdb=" N VAL C1037 " --> pdb=" O ALA C1033 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS C1039 " --> pdb=" O ASP C1035 " (cutoff:3.500A) Proline residue: C1040 - end of helix removed outlier: 3.736A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1052 No H-bonds generated for 'chain 'C' and resid 1050 through 1052' Processing helix chain 'C' and resid 1063 through 1065 No H-bonds generated for 'chain 'C' and resid 1063 through 1065' Processing helix chain 'C' and resid 1070 through 1085 Proline residue: C1074 - end of helix removed outlier: 3.808A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1124 removed outlier: 3.750A pdb=" N ILE C1106 " --> pdb=" O GLN C1102 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN C1108 " --> pdb=" O LYS C1104 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1145 removed outlier: 4.130A pdb=" N PHE C1142 " --> pdb=" O ILE C1138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C1143 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1191 Processing helix chain 'C' and resid 1193 through 1228 removed outlier: 3.525A pdb=" N ILE C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C1220 " --> pdb=" O ASP C1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 35 through 38 No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.812A pdb=" N LEU D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 58' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 117 through 125 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.620A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 4.050A pdb=" N LEU D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 removed outlier: 3.663A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.533A pdb=" N THR D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.795A pdb=" N MET D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 4.117A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.645A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'D' and resid 452 through 460 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 471 through 478 Processing helix chain 'D' and resid 487 through 496 removed outlier: 3.581A pdb=" N PHE D 490 " --> pdb=" O PRO D 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 493 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 527 through 529 No H-bonds generated for 'chain 'D' and resid 527 through 529' Processing helix chain 'D' and resid 531 through 537 Processing helix chain 'D' and resid 621 through 631 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 648 through 667 Processing helix chain 'D' and resid 675 through 700 Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 737 through 748 Processing helix chain 'D' and resid 757 through 766 Processing helix chain 'D' and resid 768 through 773 Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.545A pdb=" N PHE D 845 " --> pdb=" O ILE D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 Processing helix chain 'D' and resid 884 through 905 Processing helix chain 'D' and resid 912 through 921 Processing helix chain 'D' and resid 923 through 944 Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.590A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 999 Processing helix chain 'D' and resid 1001 through 1022 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1031 through 1045 removed outlier: 3.645A pdb=" N VAL D1037 " --> pdb=" O ALA D1033 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS D1039 " --> pdb=" O ASP D1035 " (cutoff:3.500A) Proline residue: D1040 - end of helix removed outlier: 3.736A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1052 No H-bonds generated for 'chain 'D' and resid 1050 through 1052' Processing helix chain 'D' and resid 1063 through 1065 No H-bonds generated for 'chain 'D' and resid 1063 through 1065' Processing helix chain 'D' and resid 1070 through 1085 Proline residue: D1074 - end of helix removed outlier: 3.808A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1124 removed outlier: 3.751A pdb=" N ILE D1106 " --> pdb=" O GLN D1102 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN D1108 " --> pdb=" O LYS D1104 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D1109 " --> pdb=" O ALA D1105 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.130A pdb=" N PHE D1142 " --> pdb=" O ILE D1138 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1191 Processing helix chain 'D' and resid 1193 through 1228 removed outlier: 3.524A pdb=" N ILE D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D1220 " --> pdb=" O ASP D1216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 13 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 105 through 109 removed outlier: 3.542A pdb=" N ALA A 106 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLY A 218 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 94 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASP A 220 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ASN A 96 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.819A pdb=" N LEU A 111 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 247 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 244 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 289 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 313 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 13 through 16 Processing sheet with id= E, first strand: chain 'B' and resid 105 through 109 removed outlier: 3.543A pdb=" N ALA B 106 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLY B 218 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 94 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP B 220 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ASN B 96 " --> pdb=" O ASP B 220 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.820A pdb=" N LEU B 111 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 247 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 244 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE B 289 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 313 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 13 through 16 Processing sheet with id= H, first strand: chain 'C' and resid 105 through 109 removed outlier: 3.543A pdb=" N ALA C 106 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY C 218 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL C 94 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP C 220 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ASN C 96 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 110 through 112 removed outlier: 7.819A pdb=" N LEU C 111 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU C 247 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS C 244 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE C 289 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL C 313 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 13 through 16 Processing sheet with id= K, first strand: chain 'D' and resid 105 through 109 removed outlier: 3.544A pdb=" N ALA D 106 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY D 218 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 94 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP D 220 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ASN D 96 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 110 through 112 removed outlier: 7.819A pdb=" N LEU D 111 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU D 247 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 244 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE D 289 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL D 313 " --> pdb=" O ILE D 289 " (cutoff:3.500A) 1596 hydrogen bonds defined for protein. 4500 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: 28.51 Time building geometry restraints manager: 49.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 35848 1.03 - 1.24: 4313 1.24 - 1.44: 11823 1.44 - 1.65: 22968 1.65 - 1.85: 376 Bond restraints: 75328 Sorted by residual: bond pdb=" C6 ZY8 B1312 " pdb=" C7 ZY8 B1312 " ideal model delta sigma weight residual 1.797 1.516 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C6 ZY8 D1315 " pdb=" C7 ZY8 D1315 " ideal model delta sigma weight residual 1.797 1.517 0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C6 ZY8 C1313 " pdb=" C7 ZY8 C1313 " ideal model delta sigma weight residual 1.797 1.517 0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C6 ZY8 A1314 " pdb=" C7 ZY8 A1314 " ideal model delta sigma weight residual 1.797 1.518 0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C6 ZY8 C1313 " pdb=" N5 ZY8 C1313 " ideal model delta sigma weight residual 1.759 1.506 0.253 2.00e-02 2.50e+03 1.61e+02 ... (remaining 75323 not shown) Histogram of bond angle deviations from ideal: 59.73 - 77.19: 19 77.19 - 94.65: 7 94.65 - 112.11: 83517 112.11 - 129.57: 50686 129.57 - 147.03: 375 Bond angle restraints: 134604 Sorted by residual: angle pdb=" C SER D 22 " pdb=" CA SER D 22 " pdb=" HA SER D 22 " ideal model delta sigma weight residual 109.00 69.58 39.42 3.00e+00 1.11e-01 1.73e+02 angle pdb=" N SER D 22 " pdb=" CA SER D 22 " pdb=" HA SER D 22 " ideal model delta sigma weight residual 110.00 72.70 37.30 3.00e+00 1.11e-01 1.55e+02 angle pdb=" CD2 LEU C 156 " pdb=" CG LEU C 156 " pdb=" HG LEU C 156 " ideal model delta sigma weight residual 108.00 74.16 33.84 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CB SER D 22 " pdb=" CA SER D 22 " pdb=" HA SER D 22 " ideal model delta sigma weight residual 109.00 75.25 33.75 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CD1 LEU C 156 " pdb=" CG LEU C 156 " pdb=" HG LEU C 156 " ideal model delta sigma weight residual 108.00 75.41 32.59 3.00e+00 1.11e-01 1.18e+02 ... (remaining 134599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 35648 35.28 - 70.56: 1148 70.56 - 105.84: 103 105.84 - 141.12: 45 141.12 - 176.40: 20 Dihedral angle restraints: 36964 sinusoidal: 21364 harmonic: 15600 Sorted by residual: dihedral pdb=" CA TYR D 18 " pdb=" C TYR D 18 " pdb=" N ILE D 19 " pdb=" CA ILE D 19 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA TYR B 18 " pdb=" C TYR B 18 " pdb=" N ILE B 19 " pdb=" CA ILE B 19 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR A 18 " pdb=" C TYR A 18 " pdb=" N ILE A 19 " pdb=" CA ILE A 19 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 36961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4322 0.071 - 0.143: 1142 0.143 - 0.214: 148 0.214 - 0.286: 32 0.286 - 0.357: 4 Chirality restraints: 5648 Sorted by residual: chirality pdb=" CG LEU A 156 " pdb=" CB LEU A 156 " pdb=" CD1 LEU A 156 " pdb=" CD2 LEU A 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU D 156 " pdb=" CB LEU D 156 " pdb=" CD1 LEU D 156 " pdb=" CD2 LEU D 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CG LEU B 156 " pdb=" CB LEU B 156 " pdb=" CD1 LEU B 156 " pdb=" CD2 LEU B 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5645 not shown) Planarity restraints: 10508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 177 " 0.220 2.00e-02 2.50e+03 2.71e-01 1.10e+03 pdb=" CG ASN D 177 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN D 177 " -0.218 2.00e-02 2.50e+03 pdb=" ND2 ASN D 177 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN D 177 " -0.418 2.00e-02 2.50e+03 pdb="HD22 ASN D 177 " 0.411 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 177 " 0.220 2.00e-02 2.50e+03 2.70e-01 1.10e+03 pdb=" CG ASN A 177 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 177 " -0.218 2.00e-02 2.50e+03 pdb=" ND2 ASN A 177 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN A 177 " -0.417 2.00e-02 2.50e+03 pdb="HD22 ASN A 177 " 0.410 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 177 " -0.220 2.00e-02 2.50e+03 2.70e-01 1.09e+03 pdb=" CG ASN B 177 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN B 177 " 0.218 2.00e-02 2.50e+03 pdb=" ND2 ASN B 177 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN B 177 " 0.417 2.00e-02 2.50e+03 pdb="HD22 ASN B 177 " -0.410 2.00e-02 2.50e+03 ... (remaining 10505 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 4916 2.21 - 2.81: 156492 2.81 - 3.40: 201751 3.40 - 4.00: 281352 4.00 - 4.60: 433447 Nonbonded interactions: 1077958 Sorted by model distance: nonbonded pdb=" O PRO D 484 " pdb=" HE ARG D 634 " model vdw 1.610 1.850 nonbonded pdb=" O PRO A 484 " pdb=" HE ARG A 634 " model vdw 1.611 1.850 nonbonded pdb=" O PRO C 484 " pdb=" HE ARG C 634 " model vdw 1.611 1.850 nonbonded pdb=" O PRO B 484 " pdb=" HE ARG B 634 " model vdw 1.611 1.850 nonbonded pdb=" H SER D 22 " pdb=" HA SER D 22 " model vdw 1.647 1.816 ... (remaining 1077953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 or \ resid 1308 through 1311)) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 or \ resid 1308 through 1311)) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 or \ resid 1308 through 1311)) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 or \ resid 1308 through 1311)) } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.880 Extract box with map and model: 8.440 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 182.230 Find NCS groups from input model: 3.450 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.015 0.281 39412 Z= 0.934 Angle : 1.220 19.244 52976 Z= 0.608 Chirality : 0.065 0.357 5648 Planarity : 0.007 0.057 6312 Dihedral : 18.089 176.401 16456 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.69 % Favored : 92.13 % Rotamer: Outliers : 0.31 % Allowed : 2.85 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -3.02 (0.11), residues: 4356 helix: -1.47 (0.09), residues: 2544 sheet: -3.64 (0.23), residues: 236 loop : -2.41 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP B1042 HIS 0.014 0.003 HIS A1137 PHE 0.074 0.005 PHE D 858 TYR 0.076 0.005 TYR A 870 ARG 0.015 0.002 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 555 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0704 (mtm) cc_final: 0.0184 (tmt) REVERT: A 143 MET cc_start: 0.6040 (mtm) cc_final: 0.4948 (tmt) REVERT: A 372 MET cc_start: 0.6724 (mmp) cc_final: 0.6339 (mmp) REVERT: A 392 ASP cc_start: 0.7098 (t70) cc_final: 0.6794 (t70) REVERT: A 755 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7645 (mttm) REVERT: A 911 LYS cc_start: 0.7676 (mttt) cc_final: 0.7457 (mtmt) REVERT: A 914 GLN cc_start: 0.8116 (mt0) cc_final: 0.7696 (mm110) REVERT: A 1084 GLN cc_start: 0.8584 (tp40) cc_final: 0.8123 (tp40) REVERT: A 1166 ASP cc_start: 0.7475 (m-30) cc_final: 0.7252 (m-30) REVERT: B 60 MET cc_start: 0.0638 (mtm) cc_final: 0.0119 (tmt) REVERT: B 118 GLU cc_start: 0.6085 (pm20) cc_final: 0.5743 (pp20) REVERT: B 143 MET cc_start: 0.5962 (mtm) cc_final: 0.4887 (tmt) REVERT: B 372 MET cc_start: 0.6668 (mmp) cc_final: 0.6278 (mmp) REVERT: B 392 ASP cc_start: 0.7141 (t70) cc_final: 0.6841 (t70) REVERT: B 461 ASN cc_start: 0.8333 (m110) cc_final: 0.8132 (m110) REVERT: B 755 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7480 (mttm) REVERT: B 911 LYS cc_start: 0.7585 (mttt) cc_final: 0.7232 (mtmt) REVERT: B 914 GLN cc_start: 0.8011 (mt0) cc_final: 0.7372 (mm110) REVERT: B 1084 GLN cc_start: 0.8577 (tp40) cc_final: 0.8062 (tp40) REVERT: B 1166 ASP cc_start: 0.7454 (m-30) cc_final: 0.7148 (m-30) REVERT: B 1186 ASP cc_start: 0.7178 (m-30) cc_final: 0.6911 (m-30) REVERT: B 1188 LYS cc_start: 0.7857 (tttm) cc_final: 0.7513 (ttpp) REVERT: C 60 MET cc_start: 0.0662 (mtm) cc_final: 0.0156 (tmt) REVERT: C 143 MET cc_start: 0.5996 (mtm) cc_final: 0.4890 (tmt) REVERT: C 372 MET cc_start: 0.6757 (mmp) cc_final: 0.6362 (mmp) REVERT: C 392 ASP cc_start: 0.7134 (t70) cc_final: 0.6831 (t70) REVERT: C 461 ASN cc_start: 0.8317 (m110) cc_final: 0.8085 (m110) REVERT: C 755 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7473 (mttm) REVERT: C 911 LYS cc_start: 0.7575 (mttt) cc_final: 0.7214 (mtmt) REVERT: C 914 GLN cc_start: 0.8015 (mt0) cc_final: 0.7375 (mm110) REVERT: C 1084 GLN cc_start: 0.8567 (tp40) cc_final: 0.8061 (tp40) REVERT: C 1166 ASP cc_start: 0.7496 (m-30) cc_final: 0.7168 (m-30) REVERT: C 1186 ASP cc_start: 0.7205 (m-30) cc_final: 0.6943 (m-30) REVERT: C 1188 LYS cc_start: 0.7853 (tttm) cc_final: 0.7491 (ttpp) REVERT: D 60 MET cc_start: 0.0719 (mtm) cc_final: 0.0173 (tmt) REVERT: D 130 MET cc_start: 0.7288 (mtp) cc_final: 0.7086 (mtp) REVERT: D 143 MET cc_start: 0.5961 (mtm) cc_final: 0.4812 (tmt) REVERT: D 372 MET cc_start: 0.6730 (mmp) cc_final: 0.6319 (mmp) REVERT: D 392 ASP cc_start: 0.7185 (t70) cc_final: 0.6885 (t70) REVERT: D 461 ASN cc_start: 0.8362 (m110) cc_final: 0.8139 (m110) REVERT: D 755 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7590 (mttm) REVERT: D 911 LYS cc_start: 0.7601 (mttt) cc_final: 0.7329 (mtmt) REVERT: D 914 GLN cc_start: 0.8078 (mt0) cc_final: 0.7544 (mm110) REVERT: D 1084 GLN cc_start: 0.8572 (tp40) cc_final: 0.8061 (tp40) REVERT: D 1166 ASP cc_start: 0.7473 (m-30) cc_final: 0.7205 (m-30) REVERT: D 1186 ASP cc_start: 0.7213 (m-30) cc_final: 0.6994 (m-30) REVERT: D 1188 LYS cc_start: 0.7883 (tttm) cc_final: 0.7629 (ttpp) outliers start: 12 outliers final: 0 residues processed: 567 average time/residue: 3.0799 time to fit residues: 2097.6028 Evaluate side-chains 354 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 341 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 254 optimal weight: 20.0000 chunk 395 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 183 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN A 635 GLN A 700 GLN A1084 GLN A1098 ASN A1102 GLN A1171 HIS B 3 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 183 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 635 GLN B 700 GLN B1084 GLN B1098 ASN B1102 GLN B1171 HIS C 3 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 183 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 635 GLN C 700 GLN C1084 GLN C1098 ASN C1102 GLN C1171 HIS D 3 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 183 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 635 GLN D 700 GLN D1084 GLN D1098 ASN D1102 GLN D1171 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39412 Z= 0.180 Angle : 0.656 19.824 52976 Z= 0.323 Chirality : 0.046 1.672 5648 Planarity : 0.004 0.041 6312 Dihedral : 20.007 178.675 7848 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 1.26 % Allowed : 6.40 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -1.32 (0.12), residues: 4356 helix: 0.15 (0.10), residues: 2616 sheet: -3.10 (0.25), residues: 248 loop : -2.26 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1111 HIS 0.004 0.001 HIS A 183 PHE 0.030 0.002 PHE C1118 TYR 0.022 0.002 TYR A 18 ARG 0.004 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 362 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0328 (mtm) cc_final: 0.0007 (tmt) REVERT: A 143 MET cc_start: 0.6002 (mtm) cc_final: 0.4916 (tmt) REVERT: A 368 MET cc_start: 0.5467 (mtp) cc_final: 0.5193 (mtp) REVERT: A 372 MET cc_start: 0.6731 (mmp) cc_final: 0.6390 (mmp) REVERT: A 755 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7579 (mttm) REVERT: A 911 LYS cc_start: 0.7665 (mttt) cc_final: 0.7458 (mtmt) REVERT: A 914 GLN cc_start: 0.8041 (mt0) cc_final: 0.7480 (mm110) REVERT: A 953 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 1169 LYS cc_start: 0.8260 (mttm) cc_final: 0.8008 (mtmm) REVERT: A 1184 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: A 1194 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5979 (tp30) REVERT: B 60 MET cc_start: 0.0434 (mtm) cc_final: 0.0060 (tmt) REVERT: B 143 MET cc_start: 0.5967 (mtm) cc_final: 0.4862 (tmt) REVERT: B 368 MET cc_start: 0.5433 (mtp) cc_final: 0.5105 (mtp) REVERT: B 372 MET cc_start: 0.6636 (mmp) cc_final: 0.6291 (mmp) REVERT: B 755 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7390 (mttm) REVERT: B 911 LYS cc_start: 0.7506 (mttt) cc_final: 0.7176 (mtmt) REVERT: B 914 GLN cc_start: 0.7921 (mt0) cc_final: 0.7137 (mm110) REVERT: B 922 ASP cc_start: 0.7236 (t0) cc_final: 0.6900 (m-30) REVERT: B 953 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7015 (t80) REVERT: B 1168 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7313 (mmmm) REVERT: B 1169 LYS cc_start: 0.8127 (mttm) cc_final: 0.7791 (mtmm) REVERT: B 1184 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: B 1186 ASP cc_start: 0.7168 (m-30) cc_final: 0.6917 (m-30) REVERT: B 1188 LYS cc_start: 0.7905 (tttm) cc_final: 0.7599 (ttpp) REVERT: B 1194 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: C 60 MET cc_start: 0.0430 (mtm) cc_final: 0.0059 (tmt) REVERT: C 143 MET cc_start: 0.5961 (mtm) cc_final: 0.4857 (tmt) REVERT: C 368 MET cc_start: 0.5471 (mtp) cc_final: 0.5200 (mtp) REVERT: C 372 MET cc_start: 0.6660 (mmp) cc_final: 0.6307 (mmp) REVERT: C 755 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7450 (mttm) REVERT: C 911 LYS cc_start: 0.7525 (mttt) cc_final: 0.7189 (mtmt) REVERT: C 914 GLN cc_start: 0.7918 (mt0) cc_final: 0.7144 (mm110) REVERT: C 922 ASP cc_start: 0.7241 (t0) cc_final: 0.6920 (m-30) REVERT: C 953 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7001 (t80) REVERT: C 1168 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7295 (mmmm) REVERT: C 1169 LYS cc_start: 0.8118 (mttm) cc_final: 0.7731 (mtmm) REVERT: C 1184 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: C 1186 ASP cc_start: 0.7174 (m-30) cc_final: 0.6916 (m-30) REVERT: C 1188 LYS cc_start: 0.7953 (tttm) cc_final: 0.7608 (ttpp) REVERT: C 1194 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5904 (tp30) REVERT: C 1205 GLU cc_start: 0.7697 (tt0) cc_final: 0.7494 (tt0) REVERT: D 60 MET cc_start: 0.0483 (mtm) cc_final: 0.0050 (tmt) REVERT: D 143 MET cc_start: 0.5921 (mtm) cc_final: 0.4774 (tmt) REVERT: D 368 MET cc_start: 0.4994 (mtp) cc_final: 0.4645 (mtp) REVERT: D 372 MET cc_start: 0.6608 (mmp) cc_final: 0.6236 (mmp) REVERT: D 755 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7555 (mttm) REVERT: D 911 LYS cc_start: 0.7589 (mttt) cc_final: 0.7330 (mtmt) REVERT: D 914 GLN cc_start: 0.7989 (mt0) cc_final: 0.7316 (mm110) REVERT: D 922 ASP cc_start: 0.7306 (t0) cc_final: 0.7081 (m-30) REVERT: D 953 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7090 (t80) REVERT: D 1168 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7459 (mmmm) REVERT: D 1169 LYS cc_start: 0.8199 (mttm) cc_final: 0.7883 (mtmm) REVERT: D 1184 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: D 1186 ASP cc_start: 0.7208 (m-30) cc_final: 0.6997 (m-30) REVERT: D 1188 LYS cc_start: 0.7927 (tttm) cc_final: 0.7698 (ttpp) REVERT: D 1194 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: D 1205 GLU cc_start: 0.7694 (tt0) cc_final: 0.7493 (tt0) outliers start: 49 outliers final: 8 residues processed: 391 average time/residue: 2.8447 time to fit residues: 1342.9794 Evaluate side-chains 348 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 396 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 318 optimal weight: 0.8980 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN A1097 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B1097 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C1097 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D1097 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39412 Z= 0.270 Angle : 0.675 19.923 52976 Z= 0.335 Chirality : 0.047 1.656 5648 Planarity : 0.005 0.037 6312 Dihedral : 19.601 179.361 7848 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 1.05 % Allowed : 8.13 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -0.81 (0.12), residues: 4356 helix: 0.52 (0.10), residues: 2640 sheet: -2.94 (0.25), residues: 252 loop : -1.98 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1111 HIS 0.007 0.002 HIS C1039 PHE 0.026 0.002 PHE A1118 TYR 0.024 0.002 TYR B 870 ARG 0.004 0.001 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 319 time to evaluate : 4.199 Fit side-chains REVERT: A 60 MET cc_start: 0.0417 (mtm) cc_final: -0.0209 (tpp) REVERT: A 143 MET cc_start: 0.6011 (mtm) cc_final: 0.4883 (tmt) REVERT: A 262 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7281 (tt) REVERT: A 368 MET cc_start: 0.5266 (mtp) cc_final: 0.4944 (mtp) REVERT: A 372 MET cc_start: 0.6610 (mmp) cc_final: 0.6216 (mmp) REVERT: A 501 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5696 (mt) REVERT: A 755 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7726 (mttm) REVERT: A 911 LYS cc_start: 0.7690 (mttt) cc_final: 0.7481 (mtmt) REVERT: A 914 GLN cc_start: 0.8043 (mt0) cc_final: 0.7511 (mm110) REVERT: A 953 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 1184 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: A 1194 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6238 (tp30) REVERT: B 60 MET cc_start: 0.0448 (mtm) cc_final: -0.0200 (tpp) REVERT: B 143 MET cc_start: 0.6024 (mtm) cc_final: 0.4886 (tmt) REVERT: B 372 MET cc_start: 0.6636 (mmp) cc_final: 0.4359 (mtt) REVERT: B 501 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5686 (mt) REVERT: B 755 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7546 (mttm) REVERT: B 911 LYS cc_start: 0.7556 (mttt) cc_final: 0.7224 (mtmt) REVERT: B 914 GLN cc_start: 0.7980 (mt0) cc_final: 0.7201 (mm110) REVERT: B 922 ASP cc_start: 0.7416 (t0) cc_final: 0.6966 (m-30) REVERT: B 953 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 1168 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7289 (mmmm) REVERT: B 1184 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: B 1186 ASP cc_start: 0.7294 (m-30) cc_final: 0.7049 (m-30) REVERT: B 1187 ASP cc_start: 0.7727 (m-30) cc_final: 0.7369 (m-30) REVERT: B 1188 LYS cc_start: 0.8040 (tttm) cc_final: 0.7694 (ttpp) REVERT: B 1194 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: C 60 MET cc_start: 0.0436 (mtm) cc_final: -0.0197 (tpp) REVERT: C 143 MET cc_start: 0.5986 (mtm) cc_final: 0.4852 (tmt) REVERT: C 372 MET cc_start: 0.6605 (mmp) cc_final: 0.6178 (mmp) REVERT: C 501 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5585 (mt) REVERT: C 755 LYS cc_start: 0.7970 (mtmt) cc_final: 0.7554 (mttm) REVERT: C 911 LYS cc_start: 0.7545 (mttt) cc_final: 0.7205 (mtmt) REVERT: C 914 GLN cc_start: 0.7934 (mt0) cc_final: 0.7176 (mm110) REVERT: C 922 ASP cc_start: 0.7415 (t0) cc_final: 0.6972 (m-30) REVERT: C 953 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7298 (t80) REVERT: C 1168 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7267 (mmmm) REVERT: C 1184 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: C 1186 ASP cc_start: 0.7313 (m-30) cc_final: 0.7063 (m-30) REVERT: C 1187 ASP cc_start: 0.7702 (m-30) cc_final: 0.7340 (m-30) REVERT: C 1194 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6141 (tp30) REVERT: D 60 MET cc_start: 0.0538 (mtm) cc_final: -0.0151 (tpp) REVERT: D 143 MET cc_start: 0.6007 (mtm) cc_final: 0.4799 (tmt) REVERT: D 372 MET cc_start: 0.6597 (mmp) cc_final: 0.4247 (mtt) REVERT: D 501 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5627 (mt) REVERT: D 755 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7665 (mttm) REVERT: D 911 LYS cc_start: 0.7623 (mttt) cc_final: 0.7361 (mtmt) REVERT: D 914 GLN cc_start: 0.8002 (mt0) cc_final: 0.7364 (mm110) REVERT: D 922 ASP cc_start: 0.7500 (t0) cc_final: 0.7172 (m-30) REVERT: D 953 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7357 (t80) REVERT: D 1168 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7439 (mmmm) REVERT: D 1184 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: D 1186 ASP cc_start: 0.7352 (m-30) cc_final: 0.7141 (m-30) REVERT: D 1187 ASP cc_start: 0.7810 (m-30) cc_final: 0.7481 (m-30) REVERT: D 1188 LYS cc_start: 0.8059 (tttm) cc_final: 0.7803 (ttpp) REVERT: D 1194 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6208 (tp30) outliers start: 41 outliers final: 12 residues processed: 339 average time/residue: 2.5235 time to fit residues: 1056.6757 Evaluate side-chains 336 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 307 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 398 optimal weight: 8.9990 chunk 421 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN A1137 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B1102 GLN B1137 HIS ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 461 ASN C1102 GLN C1137 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 461 ASN D1102 GLN D1137 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39412 Z= 0.250 Angle : 0.649 19.904 52976 Z= 0.318 Chirality : 0.046 1.651 5648 Planarity : 0.004 0.036 6312 Dihedral : 19.029 173.687 7848 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.05 % Allowed : 9.44 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -0.52 (0.12), residues: 4356 helix: 0.75 (0.10), residues: 2632 sheet: -2.85 (0.26), residues: 252 loop : -1.84 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1111 HIS 0.007 0.002 HIS C1137 PHE 0.029 0.002 PHE B1118 TYR 0.021 0.002 TYR C1122 ARG 0.005 0.001 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 318 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0521 (mtm) cc_final: -0.0283 (tpp) REVERT: A 143 MET cc_start: 0.6065 (mtm) cc_final: 0.4910 (tmt) REVERT: A 369 MET cc_start: 0.6670 (mmm) cc_final: 0.6116 (mmm) REVERT: A 372 MET cc_start: 0.6583 (mmp) cc_final: 0.6313 (mmp) REVERT: A 501 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5776 (mt) REVERT: A 755 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7787 (mttm) REVERT: A 911 LYS cc_start: 0.7694 (mttt) cc_final: 0.7491 (mtmt) REVERT: A 914 GLN cc_start: 0.8055 (mt0) cc_final: 0.7507 (mm110) REVERT: A 1184 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: A 1194 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: B 60 MET cc_start: 0.0545 (mtm) cc_final: -0.0262 (tpp) REVERT: B 143 MET cc_start: 0.6042 (mtm) cc_final: 0.4854 (tmt) REVERT: B 369 MET cc_start: 0.6836 (mmm) cc_final: 0.6282 (mmm) REVERT: B 372 MET cc_start: 0.6644 (mmp) cc_final: 0.6368 (mmp) REVERT: B 501 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5744 (mt) REVERT: B 755 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7614 (mttm) REVERT: B 911 LYS cc_start: 0.7535 (mttt) cc_final: 0.7210 (mtmt) REVERT: B 914 GLN cc_start: 0.7952 (mt0) cc_final: 0.7180 (mm110) REVERT: B 922 ASP cc_start: 0.7404 (t0) cc_final: 0.6945 (m-30) REVERT: B 1168 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7277 (mmmm) REVERT: B 1184 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: B 1186 ASP cc_start: 0.7334 (m-30) cc_final: 0.7093 (m-30) REVERT: B 1187 ASP cc_start: 0.7785 (m-30) cc_final: 0.7439 (m-30) REVERT: B 1188 LYS cc_start: 0.8055 (tttm) cc_final: 0.7705 (ttpp) REVERT: B 1194 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6229 (tp30) REVERT: C 143 MET cc_start: 0.6012 (mtm) cc_final: 0.4828 (tmt) REVERT: C 368 MET cc_start: 0.5239 (mtp) cc_final: 0.5021 (tmm) REVERT: C 369 MET cc_start: 0.6890 (mmm) cc_final: 0.5964 (mmm) REVERT: C 372 MET cc_start: 0.6571 (mmp) cc_final: 0.6035 (mmp) REVERT: C 501 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5667 (mt) REVERT: C 755 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7619 (mttm) REVERT: C 911 LYS cc_start: 0.7540 (mttt) cc_final: 0.7205 (mtmt) REVERT: C 914 GLN cc_start: 0.7937 (mt0) cc_final: 0.7154 (mm110) REVERT: C 922 ASP cc_start: 0.7414 (t0) cc_final: 0.6965 (m-30) REVERT: C 1168 LYS cc_start: 0.7555 (mtpp) cc_final: 0.7246 (mmmm) REVERT: C 1184 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: C 1186 ASP cc_start: 0.7338 (m-30) cc_final: 0.7093 (m-30) REVERT: C 1187 ASP cc_start: 0.7751 (m-30) cc_final: 0.7398 (m-30) REVERT: C 1188 LYS cc_start: 0.8046 (tttm) cc_final: 0.7675 (ttpp) REVERT: C 1194 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6188 (tp30) REVERT: D 60 MET cc_start: 0.0565 (mtm) cc_final: -0.0148 (tpp) REVERT: D 143 MET cc_start: 0.5989 (mtm) cc_final: 0.4756 (tmt) REVERT: D 369 MET cc_start: 0.6743 (mmm) cc_final: 0.6231 (mmm) REVERT: D 372 MET cc_start: 0.6611 (mmp) cc_final: 0.6306 (mmp) REVERT: D 501 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5724 (mt) REVERT: D 755 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7732 (mttm) REVERT: D 911 LYS cc_start: 0.7638 (mttt) cc_final: 0.7373 (mtmt) REVERT: D 914 GLN cc_start: 0.8017 (mt0) cc_final: 0.7350 (mm110) REVERT: D 922 ASP cc_start: 0.7475 (t0) cc_final: 0.7143 (m-30) REVERT: D 1168 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7423 (mmmm) REVERT: D 1184 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: D 1187 ASP cc_start: 0.7874 (m-30) cc_final: 0.7550 (m-30) REVERT: D 1188 LYS cc_start: 0.8068 (tttm) cc_final: 0.7810 (ttpp) REVERT: D 1194 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6262 (tp30) outliers start: 41 outliers final: 19 residues processed: 343 average time/residue: 2.4236 time to fit residues: 1035.3558 Evaluate side-chains 344 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 313 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 291 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C1025 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D1025 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39412 Z= 0.281 Angle : 0.661 19.989 52976 Z= 0.326 Chirality : 0.047 1.656 5648 Planarity : 0.005 0.039 6312 Dihedral : 18.964 171.561 7848 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.34 % Allowed : 9.41 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4356 helix: 0.79 (0.10), residues: 2628 sheet: -2.82 (0.27), residues: 252 loop : -1.78 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1111 HIS 0.008 0.002 HIS A1025 PHE 0.027 0.002 PHE C1118 TYR 0.022 0.002 TYR D1122 ARG 0.004 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 322 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0495 (mtm) cc_final: -0.0336 (tpp) REVERT: A 143 MET cc_start: 0.6089 (mtm) cc_final: 0.4901 (tmt) REVERT: A 368 MET cc_start: 0.5340 (mtp) cc_final: 0.5106 (mtp) REVERT: A 369 MET cc_start: 0.6668 (mmm) cc_final: 0.6169 (mmm) REVERT: A 372 MET cc_start: 0.6653 (mmp) cc_final: 0.6363 (mmp) REVERT: A 750 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (ttt90) REVERT: A 755 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7822 (mttm) REVERT: A 911 LYS cc_start: 0.7699 (mttt) cc_final: 0.7498 (mtmt) REVERT: A 914 GLN cc_start: 0.8068 (mt0) cc_final: 0.7535 (mm110) REVERT: A 953 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 1184 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: A 1194 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6382 (tp30) REVERT: B 60 MET cc_start: 0.0501 (mtm) cc_final: -0.0354 (tpp) REVERT: B 143 MET cc_start: 0.6071 (mtm) cc_final: 0.4865 (tmt) REVERT: B 369 MET cc_start: 0.6538 (mmm) cc_final: 0.6051 (mmm) REVERT: B 372 MET cc_start: 0.6619 (mmp) cc_final: 0.6339 (mmp) REVERT: B 501 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5756 (mt) REVERT: B 755 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7625 (mttm) REVERT: B 911 LYS cc_start: 0.7540 (mttt) cc_final: 0.7217 (mtmt) REVERT: B 914 GLN cc_start: 0.8007 (mt0) cc_final: 0.7229 (mm110) REVERT: B 922 ASP cc_start: 0.7437 (t0) cc_final: 0.6977 (m-30) REVERT: B 953 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7154 (t80) REVERT: B 1168 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7221 (mmmm) REVERT: B 1184 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: B 1186 ASP cc_start: 0.7411 (m-30) cc_final: 0.7147 (m-30) REVERT: B 1187 ASP cc_start: 0.7799 (m-30) cc_final: 0.7461 (m-30) REVERT: B 1188 LYS cc_start: 0.8068 (tttm) cc_final: 0.7683 (ttpp) REVERT: B 1194 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: C 60 MET cc_start: 0.2834 (OUTLIER) cc_final: 0.1826 (tpp) REVERT: C 143 MET cc_start: 0.6052 (mtm) cc_final: 0.4843 (tmt) REVERT: C 369 MET cc_start: 0.6839 (mmm) cc_final: 0.6226 (mmm) REVERT: C 372 MET cc_start: 0.6616 (mmp) cc_final: 0.4467 (mtt) REVERT: C 501 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5741 (mt) REVERT: C 755 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7664 (mttm) REVERT: C 911 LYS cc_start: 0.7544 (mttt) cc_final: 0.7210 (mtmt) REVERT: C 914 GLN cc_start: 0.7956 (mt0) cc_final: 0.7188 (mm110) REVERT: C 922 ASP cc_start: 0.7447 (t0) cc_final: 0.6998 (m-30) REVERT: C 953 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7175 (t80) REVERT: C 1168 LYS cc_start: 0.7575 (mtpp) cc_final: 0.7201 (mmmm) REVERT: C 1184 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: C 1186 ASP cc_start: 0.7413 (m-30) cc_final: 0.7146 (m-30) REVERT: C 1187 ASP cc_start: 0.7806 (m-30) cc_final: 0.7463 (m-30) REVERT: C 1188 LYS cc_start: 0.8065 (tttm) cc_final: 0.7664 (ttpp) REVERT: C 1194 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6261 (tp30) REVERT: D 60 MET cc_start: 0.0539 (mtm) cc_final: -0.0321 (tpp) REVERT: D 143 MET cc_start: 0.6021 (mtm) cc_final: 0.4772 (tmt) REVERT: D 369 MET cc_start: 0.6522 (mmm) cc_final: 0.6043 (mmm) REVERT: D 372 MET cc_start: 0.6607 (mmp) cc_final: 0.6293 (mmp) REVERT: D 501 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5771 (mt) REVERT: D 750 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7748 (ttt90) REVERT: D 755 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7758 (mttm) REVERT: D 911 LYS cc_start: 0.7632 (mttt) cc_final: 0.7379 (mtmt) REVERT: D 914 GLN cc_start: 0.8033 (mt0) cc_final: 0.7385 (mm110) REVERT: D 922 ASP cc_start: 0.7488 (t0) cc_final: 0.7166 (m-30) REVERT: D 953 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7238 (t80) REVERT: D 1168 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7375 (mmmm) REVERT: D 1184 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: D 1187 ASP cc_start: 0.7907 (m-30) cc_final: 0.7589 (m-30) REVERT: D 1188 LYS cc_start: 0.8087 (tttm) cc_final: 0.7795 (ttpp) REVERT: D 1194 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6346 (tp30) outliers start: 52 outliers final: 19 residues processed: 358 average time/residue: 2.5060 time to fit residues: 1111.3356 Evaluate side-chains 357 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 320 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 20.0000 chunk 379 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 chunk 350 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39412 Z= 0.320 Angle : 0.694 20.100 52976 Z= 0.342 Chirality : 0.048 1.632 5648 Planarity : 0.005 0.043 6312 Dihedral : 19.080 171.070 7848 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.41 % Allowed : 9.26 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -0.52 (0.13), residues: 4356 helix: 0.71 (0.10), residues: 2648 sheet: -2.85 (0.28), residues: 256 loop : -1.78 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1111 HIS 0.009 0.002 HIS C1137 PHE 0.028 0.002 PHE C1118 TYR 0.024 0.003 TYR D1122 ARG 0.004 0.001 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0502 (mtm) cc_final: -0.0375 (tpp) REVERT: A 143 MET cc_start: 0.6091 (mtm) cc_final: 0.4923 (tmt) REVERT: A 369 MET cc_start: 0.6711 (mmm) cc_final: 0.6279 (mmm) REVERT: A 372 MET cc_start: 0.6606 (mmp) cc_final: 0.6365 (mmp) REVERT: A 750 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7761 (ttt90) REVERT: A 755 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7873 (mttm) REVERT: A 911 LYS cc_start: 0.7714 (mttt) cc_final: 0.7501 (mtmt) REVERT: A 1184 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 1194 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: A 1209 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6827 (mp) REVERT: B 60 MET cc_start: 0.0524 (mtm) cc_final: -0.0366 (tpp) REVERT: B 143 MET cc_start: 0.5952 (mtm) cc_final: 0.4769 (tmt) REVERT: B 369 MET cc_start: 0.6642 (mmm) cc_final: 0.6229 (mmm) REVERT: B 372 MET cc_start: 0.6589 (mmp) cc_final: 0.6346 (mmp) REVERT: B 501 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5821 (mt) REVERT: B 755 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7691 (mttm) REVERT: B 911 LYS cc_start: 0.7593 (mttt) cc_final: 0.7250 (mtmt) REVERT: B 922 ASP cc_start: 0.7398 (t0) cc_final: 0.6950 (m-30) REVERT: B 1168 LYS cc_start: 0.7623 (mtpp) cc_final: 0.7242 (mmmm) REVERT: B 1186 ASP cc_start: 0.7418 (m-30) cc_final: 0.7144 (m-30) REVERT: B 1187 ASP cc_start: 0.7810 (m-30) cc_final: 0.7466 (m-30) REVERT: B 1188 LYS cc_start: 0.8050 (tttm) cc_final: 0.7670 (ttpp) REVERT: B 1194 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: C 60 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.1706 (ttm) REVERT: C 143 MET cc_start: 0.6014 (mtm) cc_final: 0.4833 (tmt) REVERT: C 369 MET cc_start: 0.6409 (mmm) cc_final: 0.5933 (mmm) REVERT: C 501 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5814 (mt) REVERT: C 755 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7707 (mttm) REVERT: C 911 LYS cc_start: 0.7571 (mttt) cc_final: 0.7232 (mtmt) REVERT: C 912 ILE cc_start: 0.8036 (mm) cc_final: 0.7591 (tp) REVERT: C 914 GLN cc_start: 0.7996 (mt0) cc_final: 0.7215 (mm110) REVERT: C 922 ASP cc_start: 0.7407 (t0) cc_final: 0.6968 (m-30) REVERT: C 1168 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7226 (mmmm) REVERT: C 1186 ASP cc_start: 0.7419 (m-30) cc_final: 0.7141 (m-30) REVERT: C 1187 ASP cc_start: 0.7789 (m-30) cc_final: 0.7441 (m-30) REVERT: C 1188 LYS cc_start: 0.8047 (tttm) cc_final: 0.7649 (ttpp) REVERT: C 1194 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6278 (tp30) REVERT: C 1209 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6744 (mp) REVERT: D 60 MET cc_start: 0.0572 (mtm) cc_final: -0.0349 (tpp) REVERT: D 143 MET cc_start: 0.5896 (mtm) cc_final: 0.4689 (tmt) REVERT: D 369 MET cc_start: 0.6532 (mmm) cc_final: 0.5921 (mmm) REVERT: D 501 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5832 (mt) REVERT: D 750 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7759 (ttt90) REVERT: D 755 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7813 (mttm) REVERT: D 911 LYS cc_start: 0.7649 (mttt) cc_final: 0.7392 (mtmt) REVERT: D 914 GLN cc_start: 0.8067 (mt0) cc_final: 0.7407 (mm110) REVERT: D 922 ASP cc_start: 0.7460 (t0) cc_final: 0.7142 (m-30) REVERT: D 1168 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7397 (mmmm) REVERT: D 1184 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: D 1187 ASP cc_start: 0.7899 (m-30) cc_final: 0.7580 (m-30) REVERT: D 1188 LYS cc_start: 0.8079 (tttm) cc_final: 0.7789 (ttpp) REVERT: D 1194 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6330 (tp30) outliers start: 55 outliers final: 24 residues processed: 346 average time/residue: 2.5255 time to fit residues: 1086.8115 Evaluate side-chains 339 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1209 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 308 optimal weight: 0.5980 chunk 238 optimal weight: 9.9990 chunk 355 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 420 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39412 Z= 0.229 Angle : 0.619 19.892 52976 Z= 0.305 Chirality : 0.046 1.647 5648 Planarity : 0.004 0.039 6312 Dihedral : 18.238 168.998 7848 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.98 % Allowed : 9.95 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4356 helix: 0.86 (0.10), residues: 2660 sheet: -2.57 (0.29), residues: 244 loop : -1.73 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1111 HIS 0.005 0.001 HIS B1025 PHE 0.028 0.002 PHE B1118 TYR 0.020 0.002 TYR A1122 ARG 0.003 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 309 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0690 (mtm) cc_final: 0.0179 (ptt) REVERT: A 143 MET cc_start: 0.6107 (mtm) cc_final: 0.4902 (tmt) REVERT: A 369 MET cc_start: 0.6527 (mmm) cc_final: 0.6106 (mmm) REVERT: A 372 MET cc_start: 0.6607 (mmp) cc_final: 0.4443 (mtt) REVERT: A 755 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7858 (mttm) REVERT: A 911 LYS cc_start: 0.7736 (mttt) cc_final: 0.7523 (mtmt) REVERT: A 1184 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: A 1194 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6435 (tp30) REVERT: B 60 MET cc_start: 0.0501 (mtm) cc_final: 0.0048 (ptt) REVERT: B 143 MET cc_start: 0.6078 (mtm) cc_final: 0.4850 (tmt) REVERT: B 324 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6294 (tp) REVERT: B 369 MET cc_start: 0.6683 (mmm) cc_final: 0.6003 (mmm) REVERT: B 501 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5842 (mt) REVERT: B 746 MET cc_start: 0.7500 (ttm) cc_final: 0.6885 (ttm) REVERT: B 755 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7677 (mttm) REVERT: B 911 LYS cc_start: 0.7621 (mttt) cc_final: 0.7278 (mtmt) REVERT: B 922 ASP cc_start: 0.7373 (t0) cc_final: 0.6933 (m-30) REVERT: B 1168 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7211 (mmmm) REVERT: B 1184 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: B 1186 ASP cc_start: 0.7417 (m-30) cc_final: 0.7164 (m-30) REVERT: B 1187 ASP cc_start: 0.7822 (m-30) cc_final: 0.7478 (m-30) REVERT: B 1188 LYS cc_start: 0.8046 (tttm) cc_final: 0.7666 (ttpp) REVERT: B 1194 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6336 (tp30) REVERT: B 1209 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6769 (mp) REVERT: C 60 MET cc_start: 0.3010 (OUTLIER) cc_final: 0.2007 (tpp) REVERT: C 143 MET cc_start: 0.6074 (mtm) cc_final: 0.4848 (tmt) REVERT: C 369 MET cc_start: 0.6378 (mmm) cc_final: 0.5918 (mmm) REVERT: C 372 MET cc_start: 0.6569 (mmp) cc_final: 0.4360 (mtt) REVERT: C 501 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5833 (mt) REVERT: C 755 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7700 (mttm) REVERT: C 911 LYS cc_start: 0.7550 (mttt) cc_final: 0.7219 (mtmt) REVERT: C 912 ILE cc_start: 0.8023 (mm) cc_final: 0.7580 (tp) REVERT: C 914 GLN cc_start: 0.8005 (mt0) cc_final: 0.7234 (mm110) REVERT: C 922 ASP cc_start: 0.7385 (t0) cc_final: 0.6957 (m-30) REVERT: C 1168 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7191 (mmmm) REVERT: C 1184 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: C 1186 ASP cc_start: 0.7419 (m-30) cc_final: 0.7162 (m-30) REVERT: C 1187 ASP cc_start: 0.7810 (m-30) cc_final: 0.7461 (m-30) REVERT: C 1188 LYS cc_start: 0.8045 (tttm) cc_final: 0.7647 (ttpp) REVERT: C 1194 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6318 (tp30) REVERT: D 60 MET cc_start: 0.0549 (mtm) cc_final: 0.0098 (ptt) REVERT: D 143 MET cc_start: 0.6036 (mtm) cc_final: 0.4776 (tmt) REVERT: D 369 MET cc_start: 0.6541 (mmm) cc_final: 0.6157 (mmm) REVERT: D 501 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5861 (mt) REVERT: D 746 MET cc_start: 0.7590 (ttm) cc_final: 0.7023 (ttm) REVERT: D 755 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7797 (mttm) REVERT: D 911 LYS cc_start: 0.7631 (mttt) cc_final: 0.7371 (mtmt) REVERT: D 912 ILE cc_start: 0.8150 (mm) cc_final: 0.7750 (tp) REVERT: D 914 GLN cc_start: 0.8065 (mt0) cc_final: 0.7419 (mm110) REVERT: D 922 ASP cc_start: 0.7451 (t0) cc_final: 0.7131 (m-30) REVERT: D 1168 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7365 (mmmm) REVERT: D 1184 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: D 1187 ASP cc_start: 0.7897 (m-30) cc_final: 0.7575 (m-30) REVERT: D 1188 LYS cc_start: 0.8057 (tttm) cc_final: 0.7774 (ttpp) REVERT: D 1194 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: D 1209 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6677 (mp) outliers start: 38 outliers final: 18 residues processed: 340 average time/residue: 2.5241 time to fit residues: 1059.0134 Evaluate side-chains 334 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 4.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain B residue 1209 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1209 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 250 optimal weight: 0.3980 chunk 126 optimal weight: 9.9990 chunk 82 optimal weight: 0.0570 chunk 81 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 286 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN A 914 GLN A 955 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN B 955 ASN C 27 HIS ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39412 Z= 0.170 Angle : 0.576 19.865 52976 Z= 0.281 Chirality : 0.045 1.652 5648 Planarity : 0.004 0.035 6312 Dihedral : 17.306 166.752 7848 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.00 % Allowed : 10.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -0.02 (0.13), residues: 4356 helix: 1.11 (0.10), residues: 2668 sheet: -2.43 (0.30), residues: 244 loop : -1.70 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1111 HIS 0.004 0.001 HIS A 83 PHE 0.028 0.001 PHE C1118 TYR 0.018 0.001 TYR B 759 ARG 0.004 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 312 time to evaluate : 4.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6125 (mtm) cc_final: 0.4891 (tmt) REVERT: A 369 MET cc_start: 0.6520 (mmm) cc_final: 0.6132 (mmm) REVERT: A 750 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7677 (ttt90) REVERT: A 755 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7856 (mttm) REVERT: A 911 LYS cc_start: 0.7709 (mttt) cc_final: 0.7490 (mtmt) REVERT: A 975 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7381 (ttt-90) REVERT: A 1184 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: A 1187 ASP cc_start: 0.7829 (m-30) cc_final: 0.7461 (m-30) REVERT: A 1194 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6371 (tp30) REVERT: B 143 MET cc_start: 0.6128 (mtm) cc_final: 0.4858 (tmt) REVERT: B 372 MET cc_start: 0.6726 (mmp) cc_final: 0.4733 (mtm) REVERT: B 501 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5839 (mt) REVERT: B 755 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7674 (mttm) REVERT: B 911 LYS cc_start: 0.7570 (mttt) cc_final: 0.7223 (mtmt) REVERT: B 975 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7279 (ttt-90) REVERT: B 1168 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7191 (mmmm) REVERT: B 1184 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: B 1186 ASP cc_start: 0.7372 (m-30) cc_final: 0.7133 (m-30) REVERT: B 1187 ASP cc_start: 0.7815 (m-30) cc_final: 0.7472 (m-30) REVERT: B 1188 LYS cc_start: 0.8033 (tttm) cc_final: 0.7662 (ttpp) REVERT: B 1194 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6270 (tp30) REVERT: C 60 MET cc_start: 0.2994 (OUTLIER) cc_final: 0.2025 (tpp) REVERT: C 143 MET cc_start: 0.6094 (mtm) cc_final: 0.4838 (tmt) REVERT: C 369 MET cc_start: 0.6378 (mmm) cc_final: 0.6015 (mmm) REVERT: C 372 MET cc_start: 0.6569 (mmp) cc_final: 0.6301 (mmp) REVERT: C 501 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5824 (mt) REVERT: C 755 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7694 (mttm) REVERT: C 911 LYS cc_start: 0.7495 (mttt) cc_final: 0.7154 (mtmt) REVERT: C 912 ILE cc_start: 0.7988 (mm) cc_final: 0.7533 (tp) REVERT: C 914 GLN cc_start: 0.8007 (mt0) cc_final: 0.7223 (mm110) REVERT: C 975 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7243 (ttt-90) REVERT: C 1168 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7189 (mmmm) REVERT: C 1184 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: C 1186 ASP cc_start: 0.7372 (m-30) cc_final: 0.7131 (m-30) REVERT: C 1187 ASP cc_start: 0.7800 (m-30) cc_final: 0.7452 (m-30) REVERT: C 1188 LYS cc_start: 0.8032 (tttm) cc_final: 0.7642 (ttpp) REVERT: C 1194 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6249 (tp30) REVERT: D 143 MET cc_start: 0.6052 (mtm) cc_final: 0.4761 (tmt) REVERT: D 372 MET cc_start: 0.6819 (mmp) cc_final: 0.4946 (mtm) REVERT: D 501 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5851 (mt) REVERT: D 750 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7687 (ttt90) REVERT: D 755 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7795 (mttm) REVERT: D 911 LYS cc_start: 0.7597 (mttt) cc_final: 0.7337 (mtmt) REVERT: D 912 ILE cc_start: 0.8130 (mm) cc_final: 0.7716 (tp) REVERT: D 914 GLN cc_start: 0.8068 (mt0) cc_final: 0.7413 (mm110) REVERT: D 975 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7380 (ttt-90) REVERT: D 1168 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7343 (mmmm) REVERT: D 1184 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: D 1187 ASP cc_start: 0.7854 (m-30) cc_final: 0.7538 (m-30) REVERT: D 1188 LYS cc_start: 0.8049 (tttm) cc_final: 0.7771 (ttpp) REVERT: D 1194 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6303 (tp30) outliers start: 39 outliers final: 13 residues processed: 342 average time/residue: 2.5436 time to fit residues: 1072.4207 Evaluate side-chains 340 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 4.9990 chunk 402 optimal weight: 4.9990 chunk 367 optimal weight: 9.9990 chunk 391 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 353 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39412 Z= 0.214 Angle : 0.608 19.889 52976 Z= 0.298 Chirality : 0.046 1.652 5648 Planarity : 0.004 0.037 6312 Dihedral : 17.462 163.899 7848 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.95 % Allowed : 10.57 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: 0.03 (0.13), residues: 4356 helix: 1.16 (0.10), residues: 2636 sheet: -2.34 (0.30), residues: 244 loop : -1.63 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1111 HIS 0.005 0.001 HIS A1117 PHE 0.027 0.002 PHE D1118 TYR 0.021 0.002 TYR A1122 ARG 0.002 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 306 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.0913 (OUTLIER) cc_final: -0.0505 (tpp) REVERT: A 143 MET cc_start: 0.6114 (mtm) cc_final: 0.4915 (tmt) REVERT: A 369 MET cc_start: 0.6518 (mmm) cc_final: 0.6166 (mmm) REVERT: A 372 MET cc_start: 0.6610 (mmp) cc_final: 0.6361 (mmp) REVERT: A 750 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (ttt90) REVERT: A 755 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7861 (mttm) REVERT: A 911 LYS cc_start: 0.7723 (mttt) cc_final: 0.7508 (mtmt) REVERT: A 1184 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: A 1194 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: B 60 MET cc_start: 0.1024 (OUTLIER) cc_final: -0.0450 (tpp) REVERT: B 143 MET cc_start: 0.6114 (mtm) cc_final: 0.4873 (tmt) REVERT: B 372 MET cc_start: 0.6726 (mmp) cc_final: 0.4683 (mtm) REVERT: B 501 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5822 (mt) REVERT: B 746 MET cc_start: 0.7468 (ttm) cc_final: 0.6749 (ttm) REVERT: B 755 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7678 (mttm) REVERT: B 911 LYS cc_start: 0.7590 (mttt) cc_final: 0.7244 (mtmt) REVERT: B 922 ASP cc_start: 0.7328 (t0) cc_final: 0.6893 (m-30) REVERT: B 1168 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7206 (mmmm) REVERT: B 1184 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: B 1186 ASP cc_start: 0.7398 (m-30) cc_final: 0.7141 (m-30) REVERT: B 1187 ASP cc_start: 0.7795 (m-30) cc_final: 0.7454 (m-30) REVERT: B 1188 LYS cc_start: 0.8061 (tttm) cc_final: 0.7675 (ttpp) REVERT: B 1194 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: B 1209 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6753 (mp) REVERT: C 60 MET cc_start: 0.2997 (OUTLIER) cc_final: 0.2015 (tpp) REVERT: C 143 MET cc_start: 0.6106 (mtm) cc_final: 0.4859 (tmt) REVERT: C 369 MET cc_start: 0.6353 (mmm) cc_final: 0.5969 (mmm) REVERT: C 372 MET cc_start: 0.6586 (mmp) cc_final: 0.4368 (mtt) REVERT: C 501 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5814 (mt) REVERT: C 755 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7698 (mttm) REVERT: C 911 LYS cc_start: 0.7511 (mttt) cc_final: 0.7173 (mtmt) REVERT: C 914 GLN cc_start: 0.7998 (mt0) cc_final: 0.7227 (mm110) REVERT: C 1168 LYS cc_start: 0.7574 (mtpp) cc_final: 0.7189 (mmmm) REVERT: C 1184 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: C 1186 ASP cc_start: 0.7399 (m-30) cc_final: 0.7139 (m-30) REVERT: C 1187 ASP cc_start: 0.7772 (m-30) cc_final: 0.7428 (m-30) REVERT: C 1188 LYS cc_start: 0.8052 (tttm) cc_final: 0.7653 (ttpp) REVERT: C 1194 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6265 (tp30) REVERT: D 60 MET cc_start: 0.1016 (OUTLIER) cc_final: -0.0396 (tpp) REVERT: D 143 MET cc_start: 0.6065 (mtm) cc_final: 0.4780 (tmt) REVERT: D 501 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5864 (mt) REVERT: D 746 MET cc_start: 0.7559 (ttm) cc_final: 0.6889 (ttm) REVERT: D 750 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7728 (ttt90) REVERT: D 755 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7801 (mttm) REVERT: D 911 LYS cc_start: 0.7610 (mttt) cc_final: 0.7348 (mtmt) REVERT: D 912 ILE cc_start: 0.8150 (mm) cc_final: 0.7741 (tp) REVERT: D 914 GLN cc_start: 0.8063 (mt0) cc_final: 0.7414 (mm110) REVERT: D 955 ASN cc_start: 0.7801 (t0) cc_final: 0.7193 (m110) REVERT: D 1168 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7359 (mmmm) REVERT: D 1184 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: D 1187 ASP cc_start: 0.7876 (m-30) cc_final: 0.7555 (m-30) REVERT: D 1188 LYS cc_start: 0.8070 (tttm) cc_final: 0.7785 (ttpp) REVERT: D 1194 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6318 (tp30) REVERT: D 1209 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6672 (mp) outliers start: 37 outliers final: 17 residues processed: 334 average time/residue: 2.5878 time to fit residues: 1068.9363 Evaluate side-chains 341 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain B residue 1209 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 10.0000 chunk 414 optimal weight: 3.9990 chunk 252 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 434 optimal weight: 10.0000 chunk 399 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 267 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39412 Z= 0.201 Angle : 0.591 19.860 52976 Z= 0.289 Chirality : 0.045 1.653 5648 Planarity : 0.004 0.036 6312 Dihedral : 17.192 160.965 7848 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.08 % Allowed : 10.29 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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 (0.13), residues: 4356 helix: 1.21 (0.10), residues: 2640 sheet: -2.18 (0.30), residues: 244 loop : -1.63 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1111 HIS 0.004 0.001 HIS C1137 PHE 0.027 0.002 PHE A1118 TYR 0.019 0.002 TYR D1122 ARG 0.002 0.000 ARG D 942 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 318 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6201 (mtm) cc_final: 0.4986 (tmt) REVERT: A 369 MET cc_start: 0.6382 (mmm) cc_final: 0.6083 (mmm) REVERT: A 372 MET cc_start: 0.6609 (mmp) cc_final: 0.6357 (mmp) REVERT: A 750 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7705 (ttt90) REVERT: A 755 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7852 (mttm) REVERT: A 911 LYS cc_start: 0.7709 (mttt) cc_final: 0.7487 (mtmt) REVERT: A 955 ASN cc_start: 0.7817 (t0) cc_final: 0.7331 (m110) REVERT: A 1184 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 1187 ASP cc_start: 0.7821 (m-30) cc_final: 0.7468 (m-30) REVERT: A 1194 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: B 143 MET cc_start: 0.6143 (mtm) cc_final: 0.4913 (tmt) REVERT: B 372 MET cc_start: 0.6680 (mmp) cc_final: 0.4660 (mtm) REVERT: B 755 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7670 (mttm) REVERT: B 911 LYS cc_start: 0.7584 (mttt) cc_final: 0.7227 (mtmt) REVERT: B 922 ASP cc_start: 0.7321 (t0) cc_final: 0.6897 (m-30) REVERT: B 1168 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7202 (mmmm) REVERT: B 1184 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: B 1186 ASP cc_start: 0.7396 (m-30) cc_final: 0.7139 (m-30) REVERT: B 1187 ASP cc_start: 0.7796 (m-30) cc_final: 0.7453 (m-30) REVERT: B 1188 LYS cc_start: 0.8054 (tttm) cc_final: 0.7667 (ttpp) REVERT: B 1194 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: B 1209 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6707 (mp) REVERT: C 60 MET cc_start: 0.2831 (OUTLIER) cc_final: 0.1982 (tpp) REVERT: C 143 MET cc_start: 0.6167 (mtm) cc_final: 0.4932 (tmt) REVERT: C 369 MET cc_start: 0.6366 (mmm) cc_final: 0.6045 (mmm) REVERT: C 372 MET cc_start: 0.6579 (mmp) cc_final: 0.4375 (mtt) REVERT: C 755 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7692 (mttm) REVERT: C 911 LYS cc_start: 0.7519 (mttt) cc_final: 0.7176 (mtmt) REVERT: C 912 ILE cc_start: 0.8018 (mm) cc_final: 0.7565 (tp) REVERT: C 914 GLN cc_start: 0.8000 (mt0) cc_final: 0.7228 (mm110) REVERT: C 1168 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7181 (mmmm) REVERT: C 1184 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: C 1186 ASP cc_start: 0.7397 (m-30) cc_final: 0.7136 (m-30) REVERT: C 1187 ASP cc_start: 0.7781 (m-30) cc_final: 0.7432 (m-30) REVERT: C 1188 LYS cc_start: 0.8047 (tttm) cc_final: 0.7647 (ttpp) REVERT: C 1194 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: D 143 MET cc_start: 0.6092 (mtm) cc_final: 0.4819 (tmt) REVERT: D 750 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7713 (ttt90) REVERT: D 755 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7790 (mttm) REVERT: D 911 LYS cc_start: 0.7603 (mttt) cc_final: 0.7340 (mtmt) REVERT: D 912 ILE cc_start: 0.8151 (mm) cc_final: 0.7740 (tp) REVERT: D 914 GLN cc_start: 0.8059 (mt0) cc_final: 0.7414 (mm110) REVERT: D 1168 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7354 (mmmm) REVERT: D 1184 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: D 1187 ASP cc_start: 0.7865 (m-30) cc_final: 0.7547 (m-30) REVERT: D 1188 LYS cc_start: 0.8068 (tttm) cc_final: 0.7783 (ttpp) REVERT: D 1194 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6316 (tp30) REVERT: D 1209 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6670 (mp) outliers start: 42 outliers final: 24 residues processed: 351 average time/residue: 2.5016 time to fit residues: 1090.5897 Evaluate side-chains 348 residues out of total 3888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 975 ARG Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1184 GLU Chi-restraints excluded: chain B residue 1194 GLU Chi-restraints excluded: chain B residue 1209 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 975 ARG Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 750 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 975 ARG Chi-restraints excluded: chain D residue 1184 GLU Chi-restraints excluded: chain D residue 1194 GLU Chi-restraints excluded: chain D residue 1209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 355 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.203735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129657 restraints weight = 96149.780| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.82 r_work: 0.3187 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39412 Z= 0.254 Angle : 0.635 20.037 52976 Z= 0.312 Chirality : 0.047 1.664 5648 Planarity : 0.004 0.038 6312 Dihedral : 17.547 163.444 7848 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.90 % Allowed : 10.57 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % 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: -0.02 (0.13), residues: 4356 helix: 1.09 (0.10), residues: 2644 sheet: -2.17 (0.31), residues: 244 loop : -1.65 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1111 HIS 0.006 0.001 HIS B1137 PHE 0.027 0.002 PHE D1118 TYR 0.023 0.002 TYR A1122 ARG 0.003 0.000 ARG C 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20900.24 seconds wall clock time: 361 minutes 10.74 seconds (21670.74 seconds total)