Starting phenix.real_space_refine on Sun Mar 24 14:44:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgi_31582/03_2024/7fgi_31582_updated.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 Zn 12 6.06 5 P 60 5.49 5 Mg 12 5.21 5 S 336 5.16 5 C 26520 2.51 5 N 7248 2.21 5 O 8100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E GLU 405": "OE1" <-> "OE2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G ARG 399": "NH1" <-> "NH2" Residue "G GLU 405": "OE1" <-> "OE2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H GLU 353": "OE1" <-> "OE2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H GLU 405": "OE1" <-> "OE2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I GLU 353": "OE1" <-> "OE2" Residue "I ARG 399": "NH1" <-> "NH2" Residue "I GLU 405": "OE1" <-> "OE2" Residue "I ARG 467": "NH1" <-> "NH2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J GLU 405": "OE1" <-> "OE2" Residue "J ARG 467": "NH1" <-> "NH2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K GLU 234": "OE1" <-> "OE2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K GLU 353": "OE1" <-> "OE2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K GLU 405": "OE1" <-> "OE2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L GLU 234": "OE1" <-> "OE2" Residue "L ARG 238": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "L ARG 289": "NH1" <-> "NH2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L GLU 405": "OE1" <-> "OE2" Residue "L ARG 467": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42288 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "B" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "C" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "D" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "E" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "F" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "G" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "H" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "I" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "J" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "K" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "L" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN A1001 " pdbres="SAH A1002 " Not linked: pdbres="SAH A1002 " pdbres="GTA A1003 " Not linked: pdbres="GTA A1003 " pdbres=" U A1004 " Not linked: pdbres=" G A1005 " pdbres=" MG A1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN B1001 " pdbres="SAH B1002 " Not linked: pdbres="SAH B1002 " pdbres="GTA B1003 " Not linked: pdbres="GTA B1003 " pdbres=" U B1004 " Not linked: pdbres=" G B1005 " pdbres=" MG B1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN C1001 " pdbres="SAH C1002 " Not linked: pdbres="SAH C1002 " pdbres="GTA C1003 " Not linked: pdbres="GTA C1003 " pdbres=" U C1004 " Not linked: pdbres=" G C1005 " pdbres=" MG C1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN D1001 " pdbres="SAH D1002 " Not linked: pdbres="SAH D1002 " pdbres="GTA D1003 " Not linked: pdbres="GTA D1003 " pdbres=" U D1004 " Not linked: pdbres=" G D1005 " pdbres=" MG D1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN E1001 " pdbres="SAH E1002 " Not linked: pdbres="SAH E1002 " pdbres="GTA E1003 " Not linked: pdbres="GTA E1003 " pdbres=" U E1004 " Not linked: pdbres=" G E1005 " pdbres=" MG E1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN F1001 " pdbres="SAH F1002 " Not linked: pdbres="SAH F1002 " pdbres="GTA F1003 " Not linked: pdbres="GTA F1003 " pdbres=" U F1004 " Not linked: pdbres=" G F1005 " pdbres=" MG F1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN G1001 " pdbres="SAH G1002 " Not linked: pdbres="SAH G1002 " pdbres="GTA G1003 " Not linked: pdbres="GTA G1003 " pdbres=" U G1004 " Not linked: pdbres=" G G1005 " pdbres=" MG G1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN H1001 " pdbres="SAH H1002 " Not linked: pdbres="SAH H1002 " pdbres="GTA H1003 " Not linked: pdbres="GTA H1003 " pdbres=" U H1004 " Not linked: pdbres=" G H1005 " pdbres=" MG H1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN I1001 " pdbres="SAH I1002 " Not linked: pdbres="SAH I1002 " pdbres="GTA I1003 " Not linked: pdbres="GTA I1003 " pdbres=" U I1004 " Not linked: pdbres=" G I1005 " pdbres=" MG I1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN J1001 " pdbres="SAH J1002 " Not linked: pdbres="SAH J1002 " pdbres="GTA J1003 " Not linked: pdbres="GTA J1003 " pdbres=" U J1004 " Not linked: pdbres=" G J1005 " pdbres=" MG J1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN K1001 " pdbres="SAH K1002 " Not linked: pdbres="SAH K1002 " pdbres="GTA K1003 " Not linked: pdbres="GTA K1003 " pdbres=" U K1004 " Not linked: pdbres=" G K1005 " pdbres=" MG K1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN L1001 " pdbres="SAH L1002 " Not linked: pdbres="SAH L1002 " pdbres="GTA L1003 " Not linked: pdbres="GTA L1003 " pdbres=" U L1004 " Not linked: pdbres=" G L1005 " pdbres=" MG L1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 134 44.094 168.197 61.283 1.00 0.00 S ATOM 1071 SG CYS A 141 46.875 170.987 61.145 1.00 0.00 S ATOM 4440 SG CYS B 134 18.759 130.392 61.286 1.00 0.00 S ATOM 4492 SG CYS B 141 19.774 134.199 61.149 1.00 0.00 S ATOM 7861 SG CYS C 134 15.730 84.976 61.290 1.00 0.00 S ATOM 7913 SG CYS C 141 14.705 88.779 61.152 1.00 0.00 S ATOM 11282 SG CYS D 134 35.805 44.127 61.292 1.00 0.00 S ATOM 11334 SG CYS D 141 33.015 46.908 61.155 1.00 0.00 S ATOM 14703 SG CYS E 134 73.618 18.797 61.294 1.00 0.00 S ATOM 14755 SG CYS E 141 69.811 19.811 61.157 1.00 0.00 S ATOM 18124 SG CYS F 134 119.035 15.759 61.293 1.00 0.00 S ATOM 18176 SG CYS F 141 115.232 14.733 61.156 1.00 0.00 S ATOM 21545 SG CYS G 134 159.874 35.837 61.291 1.00 0.00 S ATOM 21597 SG CYS G 141 157.094 33.048 61.154 1.00 0.00 S ATOM 24966 SG CYS H 134 185.213 73.657 61.287 1.00 0.00 S ATOM 25018 SG CYS H 141 184.199 69.850 61.151 1.00 0.00 S ATOM 28387 SG CYS I 134 188.252 119.063 61.284 1.00 0.00 S ATOM 28439 SG CYS I 141 189.278 115.260 61.147 1.00 0.00 S ATOM 31808 SG CYS J 134 168.164 159.908 61.281 1.00 0.00 S ATOM 31860 SG CYS J 141 170.954 157.127 61.144 1.00 0.00 S ATOM 35229 SG CYS K 134 130.354 185.252 61.280 1.00 0.00 S ATOM 35281 SG CYS K 141 134.161 184.238 61.143 1.00 0.00 S ATOM 38650 SG CYS L 134 84.947 188.281 61.280 1.00 0.00 S ATOM 38702 SG CYS L 141 88.751 189.306 61.143 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 41.63, per 1000 atoms: 0.98 Number of scatterers: 42288 At special positions: 0 Unit cell: (204.85, 204.85, 90.1, 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) Zn 12 29.99 S 336 16.00 P 60 15.00 Mg 12 11.99 O 8100 8.00 N 7248 7.00 C 26520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.62 Conformation dependent library (CDL) restraints added in 15.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 60 sheets defined 31.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 381 through 403 Proline residue: A 385 - end of helix removed outlier: 3.770A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 392 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 38 through 54 Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 381 through 403 Proline residue: B 385 - end of helix removed outlier: 3.770A pdb=" N ALA B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 392 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 381 through 403 Proline residue: C 385 - end of helix removed outlier: 3.771A pdb=" N ALA C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 391 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 392 " --> pdb=" O GLN C 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 352 through 362 Processing helix chain 'D' and resid 381 through 403 Proline residue: D 385 - end of helix removed outlier: 3.771A pdb=" N ALA D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 391 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 392 " --> pdb=" O GLN D 389 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 362 Processing helix chain 'E' and resid 381 through 403 Proline residue: E 385 - end of helix removed outlier: 3.770A pdb=" N ALA E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE E 391 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 392 " --> pdb=" O GLN E 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 400 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 38 through 54 Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 352 through 362 Processing helix chain 'F' and resid 381 through 403 Proline residue: F 385 - end of helix removed outlier: 3.771A pdb=" N ALA F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE F 391 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 392 " --> pdb=" O GLN F 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS F 400 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.831A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 362 Processing helix chain 'G' and resid 381 through 403 Proline residue: G 385 - end of helix removed outlier: 3.771A pdb=" N ALA G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE G 391 " --> pdb=" O ALA G 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER G 392 " --> pdb=" O GLN G 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS G 400 " --> pdb=" O GLU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 89 through 102 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 Processing helix chain 'H' and resid 345 through 347 No H-bonds generated for 'chain 'H' and resid 345 through 347' Processing helix chain 'H' and resid 352 through 362 Processing helix chain 'H' and resid 381 through 403 Proline residue: H 385 - end of helix removed outlier: 3.771A pdb=" N ALA H 388 " --> pdb=" O PRO H 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE H 391 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER H 392 " --> pdb=" O GLN H 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS H 400 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 472 Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 362 Processing helix chain 'I' and resid 381 through 403 Proline residue: I 385 - end of helix removed outlier: 3.771A pdb=" N ALA I 388 " --> pdb=" O PRO I 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE I 391 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER I 392 " --> pdb=" O GLN I 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS I 400 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 472 Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 68 through 71 Processing helix chain 'J' and resid 89 through 102 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 352 through 362 Processing helix chain 'J' and resid 381 through 403 Proline residue: J 385 - end of helix removed outlier: 3.771A pdb=" N ALA J 388 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE J 391 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER J 392 " --> pdb=" O GLN J 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS J 400 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 472 Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 89 through 102 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.191A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 362 Processing helix chain 'K' and resid 381 through 403 Proline residue: K 385 - end of helix removed outlier: 3.771A pdb=" N ALA K 388 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE K 391 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER K 392 " --> pdb=" O GLN K 389 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS K 400 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 472 Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 38 through 54 Processing helix chain 'L' and resid 68 through 71 Processing helix chain 'L' and resid 89 through 102 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.190A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 342 Processing helix chain 'L' and resid 345 through 347 No H-bonds generated for 'chain 'L' and resid 345 through 347' Processing helix chain 'L' and resid 352 through 362 Processing helix chain 'L' and resid 381 through 403 Proline residue: L 385 - end of helix removed outlier: 3.771A pdb=" N ALA L 388 " --> pdb=" O PRO L 385 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER L 392 " --> pdb=" O GLN L 389 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 177 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 177 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.749A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 Processing sheet with id= N, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.749A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 177 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 189 through 192 Processing sheet with id= S, first strand: chain 'D' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= U, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 177 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= X, first strand: chain 'E' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= Z, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= AA, first strand: chain 'F' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 189 through 192 Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AE, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.749A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 177 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 189 through 192 Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AK, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY H 177 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 189 through 192 Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= AP, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 189 through 192 Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= AU, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.749A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY J 177 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 189 through 192 Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AZ, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.750A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 177 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 189 through 192 Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BD, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= BE, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.749A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 189 through 192 Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 334 1524 hydrogen bonds defined for protein. 3924 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: 17.47 Time building geometry restraints manager: 17.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13276 1.34 - 1.46: 7240 1.46 - 1.58: 22120 1.58 - 1.69: 120 1.69 - 1.81: 504 Bond restraints: 43260 Sorted by residual: bond pdb=" C1B GTA F1003 " pdb=" C2B GTA F1003 " ideal model delta sigma weight residual 1.277 1.527 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C1B GTA I1003 " pdb=" C2B GTA I1003 " ideal model delta sigma weight residual 1.277 1.526 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1B GTA G1003 " pdb=" C2B GTA G1003 " ideal model delta sigma weight residual 1.277 1.526 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1B GTA A1003 " pdb=" C2B GTA A1003 " ideal model delta sigma weight residual 1.277 1.526 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1B GTA J1003 " pdb=" C2B GTA J1003 " ideal model delta sigma weight residual 1.277 1.526 -0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 43255 not shown) Histogram of bond angle deviations from ideal: 89.95 - 99.30: 12 99.30 - 108.66: 3011 108.66 - 118.02: 30007 118.02 - 127.38: 25302 127.38 - 136.73: 552 Bond angle restraints: 58884 Sorted by residual: angle pdb=" CG SAH G1002 " pdb=" SD SAH G1002 " pdb=" C5' SAH G1002 " ideal model delta sigma weight residual 101.77 89.95 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG SAH I1002 " pdb=" SD SAH I1002 " pdb=" C5' SAH I1002 " ideal model delta sigma weight residual 101.77 89.96 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG SAH J1002 " pdb=" SD SAH J1002 " pdb=" C5' SAH J1002 " ideal model delta sigma weight residual 101.77 89.98 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CG SAH A1002 " pdb=" SD SAH A1002 " pdb=" C5' SAH A1002 " ideal model delta sigma weight residual 101.77 90.01 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1A GTA C1003 " pdb=" N9 GTA C1003 " pdb=" C4 GTA C1003 " ideal model delta sigma weight residual 114.98 126.74 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 58879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 22249 17.73 - 35.47: 2601 35.47 - 53.20: 770 53.20 - 70.94: 144 70.94 - 88.67: 36 Dihedral angle restraints: 25800 sinusoidal: 10344 harmonic: 15456 Sorted by residual: dihedral pdb=" CA ALA K 191 " pdb=" C ALA K 191 " pdb=" N TYR K 192 " pdb=" CA TYR K 192 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ALA J 191 " pdb=" C ALA J 191 " pdb=" N TYR J 192 " pdb=" CA TYR J 192 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA D 191 " pdb=" C ALA D 191 " pdb=" N TYR D 192 " pdb=" CA TYR D 192 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 25797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3959 0.033 - 0.066: 1784 0.066 - 0.099: 512 0.099 - 0.132: 370 0.132 - 0.165: 35 Chirality restraints: 6660 Sorted by residual: chirality pdb=" C2A GTA H1003 " pdb=" C1A GTA H1003 " pdb=" C3A GTA H1003 " pdb=" O2A GTA H1003 " both_signs ideal model delta sigma weight residual False -2.43 -2.60 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" C2A GTA E1003 " pdb=" C1A GTA E1003 " pdb=" C3A GTA E1003 " pdb=" O2A GTA E1003 " both_signs ideal model delta sigma weight residual False -2.43 -2.60 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" C2A GTA C1003 " pdb=" C1A GTA C1003 " pdb=" C3A GTA C1003 " pdb=" O2A GTA C1003 " both_signs ideal model delta sigma weight residual False -2.43 -2.60 0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 6657 not shown) Planarity restraints: 7296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 130 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO C 131 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 131 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 131 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 130 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO E 131 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 131 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 131 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 130 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO I 131 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 131 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 131 " 0.029 5.00e-02 4.00e+02 ... (remaining 7293 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 60 2.43 - 3.05: 23981 3.05 - 3.67: 56354 3.67 - 4.28: 91099 4.28 - 4.90: 154158 Nonbonded interactions: 325652 Sorted by model distance: nonbonded pdb=" O22 GTA G1003 " pdb="MG MG G1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA C1003 " pdb="MG MG C1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA F1003 " pdb="MG MG F1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA L1003 " pdb="MG MG L1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA K1003 " pdb="MG MG K1006 " model vdw 1.815 2.170 ... (remaining 325647 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 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 473 or resid 1001 throu \ gh 1006)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.420 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: 0.040 Extract box with map and model: 26.260 Check model and map are aligned: 0.790 Set scattering table: 0.430 Process input model: 150.200 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.012 0.250 43260 Z= 0.812 Angle : 0.865 11.823 58884 Z= 0.392 Chirality : 0.046 0.165 6660 Planarity : 0.005 0.052 7296 Dihedral : 16.883 88.673 15768 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.16 % Allowed : 14.82 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.11), residues: 5160 helix: 1.58 (0.14), residues: 1632 sheet: 1.27 (0.17), residues: 876 loop : -2.09 (0.09), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 421 HIS 0.004 0.001 HIS B 45 PHE 0.012 0.001 PHE I 241 TYR 0.014 0.001 TYR D 285 ARG 0.005 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 256 time to evaluate : 5.142 Fit side-chains REVERT: B 123 MET cc_start: 0.6444 (mmp) cc_final: 0.5921 (mmp) REVERT: B 424 LYS cc_start: 0.6698 (mmpt) cc_final: 0.6262 (mmmt) REVERT: E 424 LYS cc_start: 0.6673 (mmpt) cc_final: 0.6262 (mmmt) REVERT: H 424 LYS cc_start: 0.6739 (mmpt) cc_final: 0.6336 (mmmt) REVERT: K 424 LYS cc_start: 0.6691 (mmpt) cc_final: 0.6270 (mmmt) outliers start: 96 outliers final: 48 residues processed: 328 average time/residue: 1.5940 time to fit residues: 640.8652 Evaluate side-chains 275 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 5.9990 chunk 391 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 263 optimal weight: 0.0030 chunk 208 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 468 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN B 377 ASN E 377 ASN H 377 ASN J 377 ASN K 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43260 Z= 0.163 Angle : 0.526 9.105 58884 Z= 0.260 Chirality : 0.041 0.135 6660 Planarity : 0.005 0.046 7296 Dihedral : 8.316 60.264 6156 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.90 % Allowed : 16.73 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5160 helix: 2.20 (0.14), residues: 1536 sheet: 0.83 (0.14), residues: 1188 loop : -1.86 (0.10), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 421 HIS 0.003 0.001 HIS A 307 PHE 0.008 0.001 PHE G 264 TYR 0.008 0.001 TYR B 154 ARG 0.004 0.000 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 4.679 Fit side-chains REVERT: C 285 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: F 285 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: G 314 MET cc_start: 0.7932 (ttm) cc_final: 0.7693 (ttt) REVERT: I 285 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: J 314 MET cc_start: 0.7929 (ttm) cc_final: 0.7701 (ttt) REVERT: K 314 MET cc_start: 0.7877 (ttm) cc_final: 0.7628 (ttm) REVERT: L 285 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7051 (m-80) outliers start: 40 outliers final: 16 residues processed: 276 average time/residue: 1.6036 time to fit residues: 540.0247 Evaluate side-chains 252 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 389 optimal weight: 0.6980 chunk 319 optimal weight: 0.3980 chunk 129 optimal weight: 10.0000 chunk 469 optimal weight: 6.9990 chunk 507 optimal weight: 2.9990 chunk 418 optimal weight: 5.9990 chunk 465 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 376 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43260 Z= 0.179 Angle : 0.530 9.964 58884 Z= 0.269 Chirality : 0.043 0.134 6660 Planarity : 0.004 0.043 7296 Dihedral : 7.400 57.937 6108 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.83 % Allowed : 16.60 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.11), residues: 5160 helix: 2.41 (0.14), residues: 1548 sheet: 1.05 (0.15), residues: 1068 loop : -1.76 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 421 HIS 0.003 0.001 HIS K 45 PHE 0.011 0.001 PHE B 183 TYR 0.010 0.001 TYR G 192 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 5.379 Fit side-chains REVERT: B 424 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6144 (mmtt) REVERT: C 285 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: C 314 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7343 (ttt) REVERT: E 424 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6145 (mmtt) REVERT: F 285 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: F 314 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7333 (ttt) REVERT: H 424 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6153 (mmtt) REVERT: I 285 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: I 314 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7341 (ttt) REVERT: K 314 MET cc_start: 0.7913 (ttm) cc_final: 0.7683 (ttt) REVERT: K 424 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6161 (mmtt) REVERT: L 285 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: L 314 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7350 (ttt) outliers start: 37 outliers final: 18 residues processed: 270 average time/residue: 1.6904 time to fit residues: 553.5080 Evaluate side-chains 274 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 4.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 0.0270 chunk 352 optimal weight: 0.4980 chunk 243 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 471 optimal weight: 6.9990 chunk 498 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 446 optimal weight: 6.9990 chunk 134 optimal weight: 0.3980 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43260 Z= 0.191 Angle : 0.513 9.080 58884 Z= 0.266 Chirality : 0.043 0.132 6660 Planarity : 0.004 0.042 7296 Dihedral : 7.598 57.826 6106 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.17 % Allowed : 16.37 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.11), residues: 5160 helix: 2.44 (0.14), residues: 1548 sheet: 1.02 (0.15), residues: 1068 loop : -1.74 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.004 0.001 HIS C 45 PHE 0.010 0.001 PHE H 183 TYR 0.010 0.001 TYR E 285 ARG 0.002 0.000 ARG J 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 5.191 Fit side-chains REVERT: B 389 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: C 285 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: C 424 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6675 (mmpt) REVERT: E 389 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: F 285 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: H 389 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: I 285 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: K 314 MET cc_start: 0.7932 (ttm) cc_final: 0.7727 (ttt) REVERT: K 389 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: L 285 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7618 (m-80) outliers start: 52 outliers final: 14 residues processed: 289 average time/residue: 1.7221 time to fit residues: 599.7754 Evaluate side-chains 261 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 371 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 425 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 447 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 43260 Z= 0.382 Angle : 0.637 10.637 58884 Z= 0.337 Chirality : 0.048 0.141 6660 Planarity : 0.005 0.045 7296 Dihedral : 8.145 62.831 6101 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.33 % Allowed : 16.46 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5160 helix: 2.10 (0.14), residues: 1620 sheet: 0.86 (0.15), residues: 1032 loop : -1.89 (0.10), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 421 HIS 0.006 0.001 HIS K 259 PHE 0.016 0.002 PHE H 183 TYR 0.017 0.002 TYR B 285 ARG 0.005 0.001 ARG J 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 4.784 Fit side-chains REVERT: C 285 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: C 314 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7398 (ttt) REVERT: C 424 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6639 (mmpt) REVERT: D 424 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6331 (mmpt) REVERT: F 285 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: F 314 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7335 (ttt) REVERT: G 285 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: G 424 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6361 (mmpt) REVERT: H 424 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6121 (mmtt) REVERT: I 285 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: I 314 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7359 (ttt) REVERT: J 342 MET cc_start: 0.8417 (mmm) cc_final: 0.8202 (mmm) REVERT: K 314 MET cc_start: 0.8028 (ttm) cc_final: 0.7699 (ttm) REVERT: L 285 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: L 314 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7396 (ttt) outliers start: 59 outliers final: 19 residues processed: 306 average time/residue: 1.6773 time to fit residues: 623.0999 Evaluate side-chains 295 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 263 time to evaluate : 5.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 424 LYS Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 424 LYS Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 5.9990 chunk 449 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 499 optimal weight: 2.9990 chunk 414 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN C 377 ASN E 377 ASN F 377 ASN H 377 ASN I 377 ASN J 389 GLN L 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43260 Z= 0.147 Angle : 0.487 9.507 58884 Z= 0.251 Chirality : 0.041 0.129 6660 Planarity : 0.004 0.042 7296 Dihedral : 7.706 60.033 6101 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.83 % Allowed : 17.05 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.12), residues: 5160 helix: 2.31 (0.14), residues: 1596 sheet: 0.95 (0.14), residues: 1212 loop : -1.78 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 258 HIS 0.003 0.001 HIS K 259 PHE 0.008 0.001 PHE D 264 TYR 0.008 0.001 TYR E 285 ARG 0.001 0.000 ARG K 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 266 time to evaluate : 4.925 Fit side-chains REVERT: B 377 ASN cc_start: 0.7941 (m-40) cc_final: 0.7738 (m110) REVERT: C 285 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: F 285 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: H 424 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6041 (mmtt) REVERT: I 285 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: K 314 MET cc_start: 0.7910 (ttm) cc_final: 0.7666 (ttt) REVERT: L 285 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7528 (m-80) outliers start: 37 outliers final: 15 residues processed: 295 average time/residue: 1.6043 time to fit residues: 576.0404 Evaluate side-chains 280 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 260 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 364 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 420 optimal weight: 0.2980 chunk 278 optimal weight: 0.8980 chunk 497 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43260 Z= 0.151 Angle : 0.485 8.965 58884 Z= 0.250 Chirality : 0.041 0.130 6660 Planarity : 0.004 0.041 7296 Dihedral : 7.497 58.191 6101 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.72 % Allowed : 17.05 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.12), residues: 5160 helix: 2.67 (0.14), residues: 1524 sheet: 1.01 (0.14), residues: 1212 loop : -1.68 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 421 HIS 0.003 0.001 HIS E 259 PHE 0.011 0.001 PHE C 423 TYR 0.008 0.001 TYR E 285 ARG 0.002 0.000 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 262 time to evaluate : 5.459 Fit side-chains REVERT: B 377 ASN cc_start: 0.7947 (m-40) cc_final: 0.7719 (m110) REVERT: C 285 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: E 424 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6039 (mmtt) REVERT: F 285 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: H 424 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6055 (mmtt) REVERT: I 285 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: J 50 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7829 (tp) REVERT: K 314 MET cc_start: 0.7906 (ttm) cc_final: 0.7680 (ttt) REVERT: K 424 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6030 (mmtt) REVERT: L 285 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7613 (m-80) outliers start: 32 outliers final: 17 residues processed: 289 average time/residue: 1.6407 time to fit residues: 578.8851 Evaluate side-chains 288 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 5.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 338 optimal weight: 0.4980 chunk 245 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN G 389 GLN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43260 Z= 0.211 Angle : 0.524 8.068 58884 Z= 0.273 Chirality : 0.043 0.133 6660 Planarity : 0.004 0.042 7296 Dihedral : 7.612 59.346 6097 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.21 % Allowed : 16.62 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.12), residues: 5160 helix: 2.53 (0.14), residues: 1548 sheet: 1.04 (0.15), residues: 1092 loop : -1.69 (0.10), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 421 HIS 0.004 0.001 HIS B 259 PHE 0.011 0.001 PHE J 241 TYR 0.011 0.001 TYR E 285 ARG 0.002 0.000 ARG H 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 268 time to evaluate : 4.933 Fit side-chains REVERT: A 50 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7838 (tp) REVERT: B 389 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: C 285 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: C 314 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7364 (ttt) REVERT: C 424 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6534 (mmtt) REVERT: D 50 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7827 (tp) REVERT: E 389 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: E 424 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6058 (mmtt) REVERT: F 285 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: F 314 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7368 (ttt) REVERT: F 424 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6546 (mmtt) REVERT: G 50 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7820 (tp) REVERT: H 389 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: H 424 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6075 (mmtt) REVERT: I 285 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: I 314 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7367 (ttt) REVERT: I 424 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6558 (mmtt) REVERT: J 50 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7835 (tp) REVERT: K 314 MET cc_start: 0.7958 (ttm) cc_final: 0.7736 (ttt) REVERT: K 389 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: K 424 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6057 (mmtt) REVERT: L 285 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: L 314 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7352 (ttt) outliers start: 54 outliers final: 18 residues processed: 308 average time/residue: 1.6858 time to fit residues: 641.4692 Evaluate side-chains 311 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 271 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 4.9990 chunk 476 optimal weight: 8.9990 chunk 434 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 278 optimal weight: 0.5980 chunk 201 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 418 optimal weight: 0.9980 chunk 438 optimal weight: 2.9990 chunk 461 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 377 ASN C 377 ASN D 377 ASN D 389 GLN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN J 389 GLN K 377 ASN L 377 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43260 Z= 0.234 Angle : 0.542 8.521 58884 Z= 0.284 Chirality : 0.044 0.136 6660 Planarity : 0.005 0.041 7296 Dihedral : 7.766 61.159 6097 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.10 % Allowed : 16.76 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.11), residues: 5160 helix: 2.43 (0.14), residues: 1560 sheet: 1.03 (0.15), residues: 1020 loop : -1.73 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 421 HIS 0.004 0.001 HIS K 259 PHE 0.012 0.001 PHE A 241 TYR 0.013 0.001 TYR E 285 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 4.898 Fit side-chains REVERT: A 50 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7842 (tp) REVERT: B 389 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: B 424 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6075 (mmtt) REVERT: C 285 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: C 314 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: C 424 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6544 (mmtt) REVERT: D 50 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7861 (tp) REVERT: E 389 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: E 424 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6073 (mmtt) REVERT: F 285 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: F 314 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7347 (ttt) REVERT: F 424 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6544 (mmtt) REVERT: G 50 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7829 (tp) REVERT: H 389 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: H 424 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6081 (mmtt) REVERT: I 285 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: I 314 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7358 (ttt) REVERT: I 424 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6543 (mmtt) REVERT: J 50 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7845 (tp) REVERT: K 314 MET cc_start: 0.7968 (ttm) cc_final: 0.7761 (ttt) REVERT: K 389 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: K 424 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6065 (mmtt) REVERT: K 441 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: L 285 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: L 314 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7340 (ttt) outliers start: 49 outliers final: 21 residues processed: 306 average time/residue: 1.6087 time to fit residues: 606.9508 Evaluate side-chains 310 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 1.9990 chunk 490 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 514 optimal weight: 3.9990 chunk 473 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 251 optimal weight: 0.0030 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43260 Z= 0.207 Angle : 0.521 8.237 58884 Z= 0.272 Chirality : 0.043 0.133 6660 Planarity : 0.004 0.042 7296 Dihedral : 7.722 61.110 6097 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 16.76 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.11), residues: 5160 helix: 2.48 (0.14), residues: 1548 sheet: 0.98 (0.15), residues: 1092 loop : -1.70 (0.10), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 421 HIS 0.004 0.001 HIS K 259 PHE 0.011 0.001 PHE D 241 TYR 0.011 0.001 TYR E 285 ARG 0.002 0.000 ARG J 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 4.719 Fit side-chains REVERT: A 50 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7851 (tp) REVERT: B 389 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: B 424 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6065 (mmtt) REVERT: C 285 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: C 314 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7354 (ttt) REVERT: C 424 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6518 (mmtt) REVERT: D 50 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7833 (tp) REVERT: E 389 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: E 424 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6063 (mmtt) REVERT: F 285 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: F 314 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7361 (ttt) REVERT: F 424 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6515 (mmtt) REVERT: G 50 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7834 (tp) REVERT: H 389 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: H 424 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6061 (mmtt) REVERT: I 285 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: I 314 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7367 (ttt) REVERT: I 424 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6543 (mmtt) REVERT: J 50 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7855 (tp) REVERT: K 314 MET cc_start: 0.7954 (ttm) cc_final: 0.7730 (ttt) REVERT: K 389 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: K 424 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6055 (mmtt) REVERT: L 285 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: L 314 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7351 (ttt) outliers start: 48 outliers final: 19 residues processed: 305 average time/residue: 1.5515 time to fit residues: 581.2276 Evaluate side-chains 312 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 424 LYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 20.0000 chunk 436 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 377 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 410 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 421 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070787 restraints weight = 209685.984| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.10 r_work: 0.2778 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43260 Z= 0.138 Angle : 0.473 7.397 58884 Z= 0.243 Chirality : 0.041 0.127 6660 Planarity : 0.004 0.041 7296 Dihedral : 7.403 58.242 6097 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.90 % Allowed : 16.94 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.12), residues: 5160 helix: 2.67 (0.14), residues: 1524 sheet: 1.00 (0.14), residues: 1212 loop : -1.63 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 258 HIS 0.002 0.001 HIS F 157 PHE 0.008 0.001 PHE J 241 TYR 0.008 0.001 TYR E 285 ARG 0.001 0.000 ARG J 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12267.11 seconds wall clock time: 220 minutes 25.18 seconds (13225.18 seconds total)