Starting phenix.real_space_refine on Mon Mar 11 17:35:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xhi_22186/03_2024/6xhi_22186_neut_updated.pdb" } resolution = 4.19 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= -0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 126 5.16 5 C 36378 2.51 5 N 10404 2.21 5 O 11610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F GLU 477": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 459": "OE1" <-> "OE2" Residue "G GLU 477": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 459": "OE1" <-> "OE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 459": "OE1" <-> "OE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 459": "OE1" <-> "OE2" Residue "J GLU 477": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 459": "OE1" <-> "OE2" Residue "K GLU 477": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 459": "OE1" <-> "OE2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 459": "OE1" <-> "OE2" Residue "M GLU 477": "OE1" <-> "OE2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 459": "OE1" <-> "OE2" Residue "N GLU 477": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 459": "OE1" <-> "OE2" Residue "O GLU 477": "OE1" <-> "OE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 459": "OE1" <-> "OE2" Residue "P GLU 477": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 178": "OE1" <-> "OE2" Residue "Q TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 459": "OE1" <-> "OE2" Residue "Q GLU 477": "OE1" <-> "OE2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "R TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 459": "OE1" <-> "OE2" Residue "R GLU 477": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 58554 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA A 531 " pdbres="ADP A 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA B 531 " pdbres="ADP B 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA C 531 " pdbres="ADP C 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "D" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA D 531 " pdbres="ADP D 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "E" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA E 531 " pdbres="ADP E 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "F" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA F 531 " pdbres="ADP F 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA G 531 " pdbres="ADP G 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "H" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA H 531 " pdbres="ADP H 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA I 531 " pdbres="ADP I 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "J" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA J 531 " pdbres="ADP J 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "K" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA K 531 " pdbres="ADP K 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "L" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA L 531 " pdbres="ADP L 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "M" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA M 531 " pdbres="ADP M 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "N" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA N 531 " pdbres="ADP N 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA O 531 " pdbres="ADP O 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "P" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA P 531 " pdbres="ADP P 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "Q" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA Q 531 " pdbres="ADP Q 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Chain: "R" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3253 Unusual residues: {'ADP': 1} Classifications: {'peptide': 473, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 462, None: 1} Not linked: pdbres="ALA R 531 " pdbres="ADP R 601 " Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 183 Time building chain proxies: 22.60, per 1000 atoms: 0.39 Number of scatterers: 58554 At special positions: 0 Unit cell: (189.14, 188.16, 193.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 36 15.00 O 11610 8.00 N 10404 7.00 C 36378 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=0, symmetry=0 Time building additional restraints: 18.81 Conformation dependent library (CDL) restraints added in 8.7 seconds 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 126 sheets defined 54.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 181 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET A 455 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 458 " --> pdb=" O MET A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 505 through 523 Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 83 through 99 Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.927A pdb=" N TYR B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 181 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 Processing helix chain 'B' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG B 395 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Proline residue: B 433 - end of helix Processing helix chain 'B' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU B 444 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 455 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 458 " --> pdb=" O MET B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 505 through 523 Processing helix chain 'C' and resid 27 through 48 removed outlier: 3.621A pdb=" N LEU C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 181 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 271 through 289 removed outlier: 3.723A pdb=" N GLU C 278 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.832A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Proline residue: C 433 - end of helix Processing helix chain 'C' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU C 444 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET C 455 " --> pdb=" O GLY C 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 458 " --> pdb=" O MET C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 505 through 523 Processing helix chain 'D' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 181 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 271 through 289 removed outlier: 3.723A pdb=" N GLU D 278 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 Processing helix chain 'D' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 435 removed outlier: 3.832A pdb=" N LYS D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Proline residue: D 433 - end of helix Processing helix chain 'D' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 454 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET D 455 " --> pdb=" O GLY D 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA D 458 " --> pdb=" O MET D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 505 through 523 Processing helix chain 'E' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 83 through 99 Processing helix chain 'E' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 176 through 191 removed outlier: 3.927A pdb=" N TYR E 179 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'E' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU E 278 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 334 Processing helix chain 'E' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE E 454 " --> pdb=" O GLU E 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET E 455 " --> pdb=" O GLY E 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 458 " --> pdb=" O MET E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 477 Processing helix chain 'E' and resid 505 through 523 Processing helix chain 'F' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 Processing helix chain 'F' and resid 83 through 99 Processing helix chain 'F' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU F 139 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR F 179 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 181 " --> pdb=" O GLU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 216 through 218 No H-bonds generated for 'chain 'F' and resid 216 through 218' Processing helix chain 'F' and resid 271 through 289 removed outlier: 3.721A pdb=" N GLU F 278 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 334 Processing helix chain 'F' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Proline residue: F 433 - end of helix Processing helix chain 'F' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU F 444 " --> pdb=" O LEU F 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 454 " --> pdb=" O GLU F 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET F 455 " --> pdb=" O GLY F 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 458 " --> pdb=" O MET F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 477 Processing helix chain 'F' and resid 505 through 523 Processing helix chain 'G' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU G 31 " --> pdb=" O GLY G 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 103 through 123 removed outlier: 3.749A pdb=" N VAL G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU G 138 " --> pdb=" O TYR G 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 168 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR G 179 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 181 " --> pdb=" O GLU G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 216 through 218 No H-bonds generated for 'chain 'G' and resid 216 through 218' Processing helix chain 'G' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU G 278 " --> pdb=" O PHE G 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 279 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS G 285 " --> pdb=" O ILE G 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS G 288 " --> pdb=" O GLU G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 334 Processing helix chain 'G' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG G 395 " --> pdb=" O ASP G 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP G 399 " --> pdb=" O ARG G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS G 430 " --> pdb=" O LYS G 426 " (cutoff:3.500A) Proline residue: G 433 - end of helix Processing helix chain 'G' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU G 444 " --> pdb=" O LEU G 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE G 454 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET G 455 " --> pdb=" O GLY G 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA G 458 " --> pdb=" O MET G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 477 Processing helix chain 'G' and resid 505 through 523 Processing helix chain 'H' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU H 31 " --> pdb=" O GLY H 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER H 47 " --> pdb=" O GLU H 43 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 Processing helix chain 'H' and resid 83 through 99 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.749A pdb=" N VAL H 107 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP H 119 " --> pdb=" O LYS H 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS H 123 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU H 138 " --> pdb=" O TYR H 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE H 140 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 168 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 176 through 191 removed outlier: 3.927A pdb=" N TYR H 179 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 181 " --> pdb=" O GLU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 216 through 218 No H-bonds generated for 'chain 'H' and resid 216 through 218' Processing helix chain 'H' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU H 278 " --> pdb=" O PHE H 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU H 279 " --> pdb=" O LEU H 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU H 282 " --> pdb=" O GLU H 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS H 288 " --> pdb=" O GLU H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA H 312 " --> pdb=" O GLN H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 334 Processing helix chain 'H' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG H 395 " --> pdb=" O ASP H 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP H 399 " --> pdb=" O ARG H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS H 430 " --> pdb=" O LYS H 426 " (cutoff:3.500A) Proline residue: H 433 - end of helix Processing helix chain 'H' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU H 444 " --> pdb=" O LEU H 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE H 454 " --> pdb=" O GLU H 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET H 455 " --> pdb=" O GLY H 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA H 458 " --> pdb=" O MET H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 477 Processing helix chain 'H' and resid 505 through 523 Processing helix chain 'I' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU I 31 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 83 through 99 Processing helix chain 'I' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL I 107 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP I 119 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU I 139 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE I 140 " --> pdb=" O LYS I 136 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR I 179 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 181 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 216 through 218 No H-bonds generated for 'chain 'I' and resid 216 through 218' Processing helix chain 'I' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU I 278 " --> pdb=" O PHE I 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU I 279 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU I 282 " --> pdb=" O GLU I 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL I 286 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS I 288 " --> pdb=" O GLU I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 334 Processing helix chain 'I' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP I 399 " --> pdb=" O ARG I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 435 removed outlier: 3.832A pdb=" N LYS I 430 " --> pdb=" O LYS I 426 " (cutoff:3.500A) Proline residue: I 433 - end of helix Processing helix chain 'I' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU I 444 " --> pdb=" O LEU I 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE I 454 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET I 455 " --> pdb=" O GLY I 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA I 458 " --> pdb=" O MET I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 477 Processing helix chain 'I' and resid 505 through 523 Processing helix chain 'J' and resid 27 through 48 removed outlier: 3.621A pdb=" N LEU J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR J 48 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 83 through 99 Processing helix chain 'J' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 148 removed outlier: 4.231A pdb=" N GLU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE J 140 " --> pdb=" O LYS J 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 168 Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR J 179 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 181 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 216 through 218 No H-bonds generated for 'chain 'J' and resid 216 through 218' Processing helix chain 'J' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU J 278 " --> pdb=" O PHE J 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU J 282 " --> pdb=" O GLU J 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 286 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS J 288 " --> pdb=" O GLU J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA J 312 " --> pdb=" O GLN J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 334 Processing helix chain 'J' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG J 395 " --> pdb=" O ASP J 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP J 399 " --> pdb=" O ARG J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS J 430 " --> pdb=" O LYS J 426 " (cutoff:3.500A) Proline residue: J 433 - end of helix Processing helix chain 'J' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU J 444 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE J 454 " --> pdb=" O GLU J 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET J 455 " --> pdb=" O GLY J 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA J 458 " --> pdb=" O MET J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 477 Processing helix chain 'J' and resid 505 through 523 Processing helix chain 'K' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU K 31 " --> pdb=" O GLY K 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER K 47 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR K 48 " --> pdb=" O ALA K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 83 through 99 Processing helix chain 'K' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL K 107 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU K 139 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE K 140 " --> pdb=" O LYS K 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN K 146 " --> pdb=" O LEU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 168 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 176 through 191 removed outlier: 3.927A pdb=" N TYR K 179 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA K 181 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 216 through 218 No H-bonds generated for 'chain 'K' and resid 216 through 218' Processing helix chain 'K' and resid 271 through 289 removed outlier: 3.721A pdb=" N GLU K 278 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 279 " --> pdb=" O LEU K 275 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU K 282 " --> pdb=" O GLU K 278 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS K 285 " --> pdb=" O ILE K 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL K 286 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS K 288 " --> pdb=" O GLU K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA K 312 " --> pdb=" O GLN K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 334 Processing helix chain 'K' and resid 387 through 410 removed outlier: 3.770A pdb=" N ARG K 395 " --> pdb=" O ASP K 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP K 399 " --> pdb=" O ARG K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS K 430 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Proline residue: K 433 - end of helix Processing helix chain 'K' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU K 444 " --> pdb=" O LEU K 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE K 454 " --> pdb=" O GLU K 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET K 455 " --> pdb=" O GLY K 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA K 458 " --> pdb=" O MET K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 465 through 477 Processing helix chain 'K' and resid 505 through 523 Processing helix chain 'L' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU L 31 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER L 47 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR L 48 " --> pdb=" O ALA L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 83 through 99 Processing helix chain 'L' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL L 107 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP L 119 " --> pdb=" O LYS L 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 168 Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR L 179 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 181 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 216 through 218 No H-bonds generated for 'chain 'L' and resid 216 through 218' Processing helix chain 'L' and resid 271 through 289 removed outlier: 3.723A pdb=" N GLU L 278 " --> pdb=" O PHE L 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU L 279 " --> pdb=" O LEU L 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU L 282 " --> pdb=" O GLU L 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS L 285 " --> pdb=" O ILE L 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL L 286 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA L 312 " --> pdb=" O GLN L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'L' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG L 395 " --> pdb=" O ASP L 391 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP L 399 " --> pdb=" O ARG L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) Proline residue: L 433 - end of helix Processing helix chain 'L' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU L 444 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE L 454 " --> pdb=" O GLU L 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET L 455 " --> pdb=" O GLY L 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA L 458 " --> pdb=" O MET L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 477 Processing helix chain 'L' and resid 505 through 523 Processing helix chain 'M' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR M 48 " --> pdb=" O ALA M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 75 Processing helix chain 'M' and resid 83 through 99 Processing helix chain 'M' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL M 107 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR M 122 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS M 123 " --> pdb=" O ASP M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU M 138 " --> pdb=" O TYR M 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE M 140 " --> pdb=" O LYS M 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN M 146 " --> pdb=" O LEU M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 168 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR M 179 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA M 181 " --> pdb=" O GLU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 216 through 218 No H-bonds generated for 'chain 'M' and resid 216 through 218' Processing helix chain 'M' and resid 271 through 289 removed outlier: 3.723A pdb=" N GLU M 278 " --> pdb=" O PHE M 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU M 279 " --> pdb=" O LEU M 275 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU M 282 " --> pdb=" O GLU M 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS M 283 " --> pdb=" O GLU M 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS M 285 " --> pdb=" O ILE M 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL M 286 " --> pdb=" O LEU M 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS M 288 " --> pdb=" O GLU M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA M 312 " --> pdb=" O GLN M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 334 Processing helix chain 'M' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG M 395 " --> pdb=" O ASP M 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP M 399 " --> pdb=" O ARG M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Proline residue: M 433 - end of helix Processing helix chain 'M' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU M 444 " --> pdb=" O LEU M 441 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE M 454 " --> pdb=" O GLU M 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET M 455 " --> pdb=" O GLY M 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA M 458 " --> pdb=" O MET M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 465 through 477 Processing helix chain 'M' and resid 505 through 523 Processing helix chain 'N' and resid 27 through 48 removed outlier: 3.621A pdb=" N LEU N 31 " --> pdb=" O GLY N 27 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR N 48 " --> pdb=" O ALA N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 83 through 99 Processing helix chain 'N' and resid 103 through 123 removed outlier: 3.749A pdb=" N VAL N 107 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR N 122 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS N 123 " --> pdb=" O ASP N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE N 140 " --> pdb=" O LYS N 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 168 Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 176 through 191 removed outlier: 3.925A pdb=" N TYR N 179 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 181 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 216 through 218 No H-bonds generated for 'chain 'N' and resid 216 through 218' Processing helix chain 'N' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU N 278 " --> pdb=" O PHE N 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU N 282 " --> pdb=" O GLU N 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS N 283 " --> pdb=" O GLU N 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL N 286 " --> pdb=" O LEU N 282 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS N 288 " --> pdb=" O GLU N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA N 312 " --> pdb=" O GLN N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 334 Processing helix chain 'N' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG N 395 " --> pdb=" O ASP N 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP N 399 " --> pdb=" O ARG N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 419 through 435 removed outlier: 3.832A pdb=" N LYS N 430 " --> pdb=" O LYS N 426 " (cutoff:3.500A) Proline residue: N 433 - end of helix Processing helix chain 'N' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU N 444 " --> pdb=" O LEU N 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE N 454 " --> pdb=" O GLU N 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET N 455 " --> pdb=" O GLY N 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA N 458 " --> pdb=" O MET N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 477 Processing helix chain 'N' and resid 505 through 523 Processing helix chain 'O' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU O 31 " --> pdb=" O GLY O 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 75 Processing helix chain 'O' and resid 83 through 99 Processing helix chain 'O' and resid 103 through 123 removed outlier: 3.749A pdb=" N VAL O 107 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP O 119 " --> pdb=" O LYS O 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU O 120 " --> pdb=" O LYS O 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR O 122 " --> pdb=" O GLU O 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS O 123 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU O 138 " --> pdb=" O TYR O 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU O 139 " --> pdb=" O LYS O 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE O 140 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN O 146 " --> pdb=" O LEU O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 168 Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR O 179 " --> pdb=" O ALA O 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA O 181 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 216 through 218 No H-bonds generated for 'chain 'O' and resid 216 through 218' Processing helix chain 'O' and resid 271 through 289 removed outlier: 3.721A pdb=" N GLU O 278 " --> pdb=" O PHE O 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU O 279 " --> pdb=" O LEU O 275 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU O 282 " --> pdb=" O GLU O 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS O 283 " --> pdb=" O GLU O 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS O 285 " --> pdb=" O ILE O 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL O 286 " --> pdb=" O LEU O 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS O 288 " --> pdb=" O GLU O 284 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 312 removed outlier: 3.751A pdb=" N ALA O 312 " --> pdb=" O GLN O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 334 Processing helix chain 'O' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG O 395 " --> pdb=" O ASP O 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP O 399 " --> pdb=" O ARG O 395 " (cutoff:3.500A) Processing helix chain 'O' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS O 430 " --> pdb=" O LYS O 426 " (cutoff:3.500A) Proline residue: O 433 - end of helix Processing helix chain 'O' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU O 444 " --> pdb=" O LEU O 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE O 454 " --> pdb=" O GLU O 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET O 455 " --> pdb=" O GLY O 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA O 458 " --> pdb=" O MET O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 465 through 477 Processing helix chain 'O' and resid 505 through 523 Processing helix chain 'P' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR P 48 " --> pdb=" O ALA P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 75 Processing helix chain 'P' and resid 83 through 99 Processing helix chain 'P' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL P 107 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP P 119 " --> pdb=" O LYS P 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU P 120 " --> pdb=" O LYS P 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU P 121 " --> pdb=" O ALA P 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR P 122 " --> pdb=" O GLU P 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS P 123 " --> pdb=" O ASP P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU P 138 " --> pdb=" O TYR P 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU P 139 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN P 146 " --> pdb=" O LEU P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 168 Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR P 179 " --> pdb=" O ALA P 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA P 181 " --> pdb=" O GLU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 205 No H-bonds generated for 'chain 'P' and resid 203 through 205' Processing helix chain 'P' and resid 216 through 218 No H-bonds generated for 'chain 'P' and resid 216 through 218' Processing helix chain 'P' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU P 278 " --> pdb=" O PHE P 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU P 282 " --> pdb=" O GLU P 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS P 283 " --> pdb=" O GLU P 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS P 285 " --> pdb=" O ILE P 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL P 286 " --> pdb=" O LEU P 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS P 288 " --> pdb=" O GLU P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA P 312 " --> pdb=" O GLN P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 334 Processing helix chain 'P' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG P 395 " --> pdb=" O ASP P 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP P 399 " --> pdb=" O ARG P 395 " (cutoff:3.500A) Processing helix chain 'P' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS P 430 " --> pdb=" O LYS P 426 " (cutoff:3.500A) Proline residue: P 433 - end of helix Processing helix chain 'P' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU P 444 " --> pdb=" O LEU P 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE P 454 " --> pdb=" O GLU P 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET P 455 " --> pdb=" O GLY P 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA P 458 " --> pdb=" O MET P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 465 through 477 Processing helix chain 'P' and resid 505 through 523 Processing helix chain 'Q' and resid 27 through 48 removed outlier: 3.622A pdb=" N LEU Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER Q 47 " --> pdb=" O GLU Q 43 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 75 Processing helix chain 'Q' and resid 83 through 99 Processing helix chain 'Q' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 121 " --> pdb=" O ALA Q 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR Q 122 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS Q 123 " --> pdb=" O ASP Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 148 removed outlier: 4.232A pdb=" N GLU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU Q 139 " --> pdb=" O LYS Q 135 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE Q 140 " --> pdb=" O LYS Q 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN Q 146 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 168 Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR Q 179 " --> pdb=" O ALA Q 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA Q 181 " --> pdb=" O GLU Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 218 No H-bonds generated for 'chain 'Q' and resid 216 through 218' Processing helix chain 'Q' and resid 271 through 289 removed outlier: 3.722A pdb=" N GLU Q 278 " --> pdb=" O PHE Q 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 279 " --> pdb=" O LEU Q 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU Q 282 " --> pdb=" O GLU Q 278 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Q 283 " --> pdb=" O GLU Q 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS Q 285 " --> pdb=" O ILE Q 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Q 286 " --> pdb=" O LEU Q 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS Q 288 " --> pdb=" O GLU Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 312 removed outlier: 3.752A pdb=" N ALA Q 312 " --> pdb=" O GLN Q 308 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 334 Processing helix chain 'Q' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG Q 395 " --> pdb=" O ASP Q 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP Q 399 " --> pdb=" O ARG Q 395 " (cutoff:3.500A) Processing helix chain 'Q' and resid 419 through 435 removed outlier: 3.831A pdb=" N LYS Q 430 " --> pdb=" O LYS Q 426 " (cutoff:3.500A) Proline residue: Q 433 - end of helix Processing helix chain 'Q' and resid 438 through 461 removed outlier: 4.078A pdb=" N GLU Q 444 " --> pdb=" O LEU Q 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE Q 454 " --> pdb=" O GLU Q 451 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET Q 455 " --> pdb=" O GLY Q 452 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA Q 458 " --> pdb=" O MET Q 455 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 477 Processing helix chain 'Q' and resid 505 through 523 Processing helix chain 'R' and resid 27 through 48 removed outlier: 3.621A pdb=" N LEU R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 75 Processing helix chain 'R' and resid 83 through 99 Processing helix chain 'R' and resid 103 through 123 removed outlier: 3.748A pdb=" N VAL R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 148 removed outlier: 4.233A pdb=" N GLU R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU R 139 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 168 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 176 through 191 removed outlier: 3.926A pdb=" N TYR R 179 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA R 181 " --> pdb=" O GLU R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' Processing helix chain 'R' and resid 216 through 218 No H-bonds generated for 'chain 'R' and resid 216 through 218' Processing helix chain 'R' and resid 271 through 289 removed outlier: 3.723A pdb=" N GLU R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS R 283 " --> pdb=" O GLU R 279 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS R 285 " --> pdb=" O ILE R 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 312 removed outlier: 3.753A pdb=" N ALA R 312 " --> pdb=" O GLN R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 334 Processing helix chain 'R' and resid 387 through 410 removed outlier: 3.771A pdb=" N ARG R 395 " --> pdb=" O ASP R 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP R 399 " --> pdb=" O ARG R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 435 removed outlier: 3.832A pdb=" N LYS R 430 " --> pdb=" O LYS R 426 " (cutoff:3.500A) Proline residue: R 433 - end of helix Processing helix chain 'R' and resid 438 through 461 removed outlier: 4.077A pdb=" N GLU R 444 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE R 454 " --> pdb=" O GLU R 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET R 455 " --> pdb=" O GLY R 452 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA R 458 " --> pdb=" O MET R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 477 Processing helix chain 'R' and resid 505 through 523 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= C, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= D, first strand: chain 'A' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL A 378 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL A 209 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 380 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS A 211 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 382 " --> pdb=" O LYS A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= F, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL A 296 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 248 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 298 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 317 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS A 299 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 319 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 484 through 487 Processing sheet with id= H, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= I, first strand: chain 'B' and resid 56 through 59 Processing sheet with id= J, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= K, first strand: chain 'B' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL B 378 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 209 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 380 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS B 211 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 382 " --> pdb=" O LYS B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 225 through 227 Processing sheet with id= M, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL B 296 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU B 248 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 298 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 317 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS B 299 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL B 319 " --> pdb=" O CYS B 299 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 484 through 487 Processing sheet with id= O, first strand: chain 'C' and resid 23 through 25 Processing sheet with id= P, first strand: chain 'C' and resid 56 through 59 Processing sheet with id= Q, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= R, first strand: chain 'C' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL C 378 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL C 209 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 380 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS C 211 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 382 " --> pdb=" O LYS C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 225 through 227 Processing sheet with id= T, first strand: chain 'C' and resid 351 through 353 removed outlier: 6.761A pdb=" N VAL C 296 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU C 248 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 298 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 317 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS C 299 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 319 " --> pdb=" O CYS C 299 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 484 through 487 Processing sheet with id= V, first strand: chain 'D' and resid 23 through 25 Processing sheet with id= W, first strand: chain 'D' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= Y, first strand: chain 'D' and resid 206 through 211 removed outlier: 6.423A pdb=" N VAL D 378 " --> pdb=" O GLN D 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL D 209 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 380 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS D 211 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 382 " --> pdb=" O LYS D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 225 through 227 Processing sheet with id= AA, first strand: chain 'D' and resid 351 through 353 removed outlier: 6.763A pdb=" N VAL D 296 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU D 248 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE D 298 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 317 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS D 299 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 319 " --> pdb=" O CYS D 299 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 484 through 487 Processing sheet with id= AC, first strand: chain 'E' and resid 23 through 25 Processing sheet with id= AD, first strand: chain 'E' and resid 56 through 59 Processing sheet with id= AE, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AF, first strand: chain 'E' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL E 378 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL E 209 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE E 380 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS E 211 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 382 " --> pdb=" O LYS E 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'E' and resid 225 through 227 Processing sheet with id= AH, first strand: chain 'E' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL E 296 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU E 248 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE E 298 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 317 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS E 299 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 319 " --> pdb=" O CYS E 299 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 484 through 487 Processing sheet with id= AJ, first strand: chain 'F' and resid 23 through 25 Processing sheet with id= AK, first strand: chain 'F' and resid 56 through 59 Processing sheet with id= AL, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= AM, first strand: chain 'F' and resid 206 through 211 removed outlier: 6.423A pdb=" N VAL F 378 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL F 209 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE F 380 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS F 211 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE F 382 " --> pdb=" O LYS F 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'F' and resid 225 through 227 Processing sheet with id= AO, first strand: chain 'F' and resid 351 through 353 removed outlier: 6.763A pdb=" N VAL F 296 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU F 248 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE F 298 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU F 317 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS F 299 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 319 " --> pdb=" O CYS F 299 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 484 through 487 Processing sheet with id= AQ, first strand: chain 'G' and resid 23 through 25 Processing sheet with id= AR, first strand: chain 'G' and resid 56 through 59 Processing sheet with id= AS, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= AT, first strand: chain 'G' and resid 206 through 211 removed outlier: 6.425A pdb=" N VAL G 378 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL G 209 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE G 380 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS G 211 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE G 382 " --> pdb=" O LYS G 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'G' and resid 225 through 227 Processing sheet with id= AV, first strand: chain 'G' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL G 296 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU G 248 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE G 298 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU G 317 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS G 299 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL G 319 " --> pdb=" O CYS G 299 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'G' and resid 484 through 487 Processing sheet with id= AX, first strand: chain 'H' and resid 23 through 25 Processing sheet with id= AY, first strand: chain 'H' and resid 56 through 59 Processing sheet with id= AZ, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BA, first strand: chain 'H' and resid 206 through 211 removed outlier: 6.423A pdb=" N VAL H 378 " --> pdb=" O GLN H 207 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL H 209 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE H 380 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS H 211 " --> pdb=" O ILE H 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE H 382 " --> pdb=" O LYS H 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'H' and resid 225 through 227 Processing sheet with id= BC, first strand: chain 'H' and resid 351 through 353 removed outlier: 6.763A pdb=" N VAL H 296 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU H 248 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 298 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU H 317 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS H 299 " --> pdb=" O LEU H 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL H 319 " --> pdb=" O CYS H 299 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 484 through 487 Processing sheet with id= BE, first strand: chain 'I' and resid 23 through 25 Processing sheet with id= BF, first strand: chain 'I' and resid 56 through 59 Processing sheet with id= BG, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BH, first strand: chain 'I' and resid 206 through 211 removed outlier: 6.423A pdb=" N VAL I 378 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL I 209 " --> pdb=" O VAL I 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE I 380 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS I 211 " --> pdb=" O ILE I 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE I 382 " --> pdb=" O LYS I 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'I' and resid 225 through 227 Processing sheet with id= BJ, first strand: chain 'I' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL I 296 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU I 248 " --> pdb=" O VAL I 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE I 298 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU I 317 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS I 299 " --> pdb=" O LEU I 317 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL I 319 " --> pdb=" O CYS I 299 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'I' and resid 484 through 487 Processing sheet with id= BL, first strand: chain 'J' and resid 23 through 25 Processing sheet with id= BM, first strand: chain 'J' and resid 56 through 59 Processing sheet with id= BN, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BO, first strand: chain 'J' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL J 378 " --> pdb=" O GLN J 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL J 209 " --> pdb=" O VAL J 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE J 380 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS J 211 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE J 382 " --> pdb=" O LYS J 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'J' and resid 225 through 227 Processing sheet with id= BQ, first strand: chain 'J' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL J 296 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU J 248 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE J 298 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU J 317 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS J 299 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL J 319 " --> pdb=" O CYS J 299 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'J' and resid 484 through 487 Processing sheet with id= BS, first strand: chain 'K' and resid 23 through 25 Processing sheet with id= BT, first strand: chain 'K' and resid 56 through 59 Processing sheet with id= BU, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= BV, first strand: chain 'K' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL K 378 " --> pdb=" O GLN K 207 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL K 209 " --> pdb=" O VAL K 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE K 380 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS K 211 " --> pdb=" O ILE K 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE K 382 " --> pdb=" O LYS K 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'K' and resid 225 through 227 Processing sheet with id= BX, first strand: chain 'K' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL K 296 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU K 248 " --> pdb=" O VAL K 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE K 298 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU K 317 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS K 299 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL K 319 " --> pdb=" O CYS K 299 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'K' and resid 484 through 487 Processing sheet with id= BZ, first strand: chain 'L' and resid 23 through 25 Processing sheet with id= CA, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= CB, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CC, first strand: chain 'L' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL L 378 " --> pdb=" O GLN L 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL L 209 " --> pdb=" O VAL L 378 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE L 380 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS L 211 " --> pdb=" O ILE L 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE L 382 " --> pdb=" O LYS L 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'L' and resid 225 through 227 Processing sheet with id= CE, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL L 296 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU L 248 " --> pdb=" O VAL L 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE L 298 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU L 317 " --> pdb=" O VAL L 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS L 299 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL L 319 " --> pdb=" O CYS L 299 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'L' and resid 484 through 487 Processing sheet with id= CG, first strand: chain 'M' and resid 23 through 25 Processing sheet with id= CH, first strand: chain 'M' and resid 56 through 59 Processing sheet with id= CI, first strand: chain 'M' and resid 193 through 195 Processing sheet with id= CJ, first strand: chain 'M' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL M 378 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL M 209 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE M 380 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS M 211 " --> pdb=" O ILE M 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE M 382 " --> pdb=" O LYS M 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'M' and resid 225 through 227 Processing sheet with id= CL, first strand: chain 'M' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL M 296 " --> pdb=" O ALA M 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU M 248 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE M 298 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU M 317 " --> pdb=" O VAL M 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS M 299 " --> pdb=" O LEU M 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL M 319 " --> pdb=" O CYS M 299 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'M' and resid 484 through 487 Processing sheet with id= CN, first strand: chain 'N' and resid 23 through 25 Processing sheet with id= CO, first strand: chain 'N' and resid 56 through 59 Processing sheet with id= CP, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= CQ, first strand: chain 'N' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL N 378 " --> pdb=" O GLN N 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL N 209 " --> pdb=" O VAL N 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE N 380 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS N 211 " --> pdb=" O ILE N 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE N 382 " --> pdb=" O LYS N 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CQ Processing sheet with id= CR, first strand: chain 'N' and resid 225 through 227 Processing sheet with id= CS, first strand: chain 'N' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL N 296 " --> pdb=" O ALA N 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU N 248 " --> pdb=" O VAL N 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE N 298 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU N 317 " --> pdb=" O VAL N 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS N 299 " --> pdb=" O LEU N 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL N 319 " --> pdb=" O CYS N 299 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'N' and resid 484 through 487 Processing sheet with id= CU, first strand: chain 'O' and resid 23 through 25 Processing sheet with id= CV, first strand: chain 'O' and resid 56 through 59 Processing sheet with id= CW, first strand: chain 'O' and resid 193 through 195 Processing sheet with id= CX, first strand: chain 'O' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL O 378 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL O 209 " --> pdb=" O VAL O 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE O 380 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS O 211 " --> pdb=" O ILE O 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE O 382 " --> pdb=" O LYS O 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= CX Processing sheet with id= CY, first strand: chain 'O' and resid 225 through 227 Processing sheet with id= CZ, first strand: chain 'O' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL O 296 " --> pdb=" O ALA O 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU O 248 " --> pdb=" O VAL O 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE O 298 " --> pdb=" O LEU O 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU O 317 " --> pdb=" O VAL O 297 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS O 299 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 319 " --> pdb=" O CYS O 299 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'O' and resid 484 through 487 Processing sheet with id= DB, first strand: chain 'P' and resid 23 through 25 Processing sheet with id= DC, first strand: chain 'P' and resid 56 through 59 Processing sheet with id= DD, first strand: chain 'P' and resid 193 through 195 Processing sheet with id= DE, first strand: chain 'P' and resid 206 through 211 removed outlier: 6.423A pdb=" N VAL P 378 " --> pdb=" O GLN P 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL P 209 " --> pdb=" O VAL P 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE P 380 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS P 211 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE P 382 " --> pdb=" O LYS P 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DE Processing sheet with id= DF, first strand: chain 'P' and resid 225 through 227 Processing sheet with id= DG, first strand: chain 'P' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL P 296 " --> pdb=" O ALA P 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU P 248 " --> pdb=" O VAL P 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE P 298 " --> pdb=" O LEU P 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU P 317 " --> pdb=" O VAL P 297 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS P 299 " --> pdb=" O LEU P 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL P 319 " --> pdb=" O CYS P 299 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'P' and resid 484 through 487 Processing sheet with id= DI, first strand: chain 'Q' and resid 23 through 25 Processing sheet with id= DJ, first strand: chain 'Q' and resid 56 through 59 Processing sheet with id= DK, first strand: chain 'Q' and resid 193 through 195 Processing sheet with id= DL, first strand: chain 'Q' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL Q 378 " --> pdb=" O GLN Q 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL Q 209 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE Q 380 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS Q 211 " --> pdb=" O ILE Q 380 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE Q 382 " --> pdb=" O LYS Q 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DL Processing sheet with id= DM, first strand: chain 'Q' and resid 225 through 227 Processing sheet with id= DN, first strand: chain 'Q' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL Q 296 " --> pdb=" O ALA Q 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU Q 248 " --> pdb=" O VAL Q 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE Q 298 " --> pdb=" O LEU Q 248 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU Q 317 " --> pdb=" O VAL Q 297 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS Q 299 " --> pdb=" O LEU Q 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL Q 319 " --> pdb=" O CYS Q 299 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'Q' and resid 484 through 487 Processing sheet with id= DP, first strand: chain 'R' and resid 23 through 25 Processing sheet with id= DQ, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= DR, first strand: chain 'R' and resid 193 through 195 Processing sheet with id= DS, first strand: chain 'R' and resid 206 through 211 removed outlier: 6.424A pdb=" N VAL R 378 " --> pdb=" O GLN R 207 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL R 209 " --> pdb=" O VAL R 378 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE R 380 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS R 211 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE R 382 " --> pdb=" O LYS R 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= DS Processing sheet with id= DT, first strand: chain 'R' and resid 225 through 227 Processing sheet with id= DU, first strand: chain 'R' and resid 351 through 353 removed outlier: 6.762A pdb=" N VAL R 296 " --> pdb=" O ALA R 246 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU R 248 " --> pdb=" O VAL R 296 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE R 298 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU R 317 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS R 299 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL R 319 " --> pdb=" O CYS R 299 " (cutoff:3.500A) Processing sheet with id= DV, first strand: chain 'R' and resid 484 through 487 3438 hydrogen bonds defined for protein. 8208 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: 26.31 Time building geometry restraints manager: 20.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 11439 1.31 - 1.44: 11835 1.44 - 1.56: 35388 1.56 - 1.68: 54 1.68 - 1.81: 252 Bond restraints: 58968 Sorted by residual: bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C4 ADP K 601 " pdb=" C5 ADP K 601 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C4 ADP R 601 " pdb=" C5 ADP R 601 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C4 ADP O 601 " pdb=" C5 ADP O 601 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C4 ADP J 601 " pdb=" C5 ADP J 601 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 58963 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.34: 810 105.34 - 112.48: 29764 112.48 - 119.63: 21798 119.63 - 126.77: 27273 126.77 - 133.91: 527 Bond angle restraints: 80172 Sorted by residual: angle pdb=" C GLU Q 394 " pdb=" N ARG Q 395 " pdb=" CA ARG Q 395 " ideal model delta sigma weight residual 120.28 126.98 -6.70 1.44e+00 4.82e-01 2.16e+01 angle pdb=" C GLU C 394 " pdb=" N ARG C 395 " pdb=" CA ARG C 395 " ideal model delta sigma weight residual 120.28 126.95 -6.67 1.44e+00 4.82e-01 2.15e+01 angle pdb=" C GLU N 394 " pdb=" N ARG N 395 " pdb=" CA ARG N 395 " ideal model delta sigma weight residual 120.28 126.95 -6.67 1.44e+00 4.82e-01 2.15e+01 angle pdb=" C GLU O 394 " pdb=" N ARG O 395 " pdb=" CA ARG O 395 " ideal model delta sigma weight residual 120.28 126.95 -6.67 1.44e+00 4.82e-01 2.14e+01 angle pdb=" C GLU E 394 " pdb=" N ARG E 395 " pdb=" CA ARG E 395 " ideal model delta sigma weight residual 120.28 126.94 -6.66 1.44e+00 4.82e-01 2.14e+01 ... (remaining 80167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 34478 27.07 - 54.15: 1000 54.15 - 81.22: 72 81.22 - 108.30: 18 108.30 - 135.37: 54 Dihedral angle restraints: 35622 sinusoidal: 11376 harmonic: 24246 Sorted by residual: dihedral pdb=" O2A ADP M 601 " pdb=" O3A ADP M 601 " pdb=" PA ADP M 601 " pdb=" PB ADP M 601 " ideal model delta sinusoidal sigma weight residual -60.00 75.37 -135.37 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O2A ADP K 601 " pdb=" O3A ADP K 601 " pdb=" PA ADP K 601 " pdb=" PB ADP K 601 " ideal model delta sinusoidal sigma weight residual -60.00 75.32 -135.32 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O2A ADP L 601 " pdb=" O3A ADP L 601 " pdb=" PA ADP L 601 " pdb=" PB ADP L 601 " ideal model delta sinusoidal sigma weight residual -60.00 75.32 -135.32 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 35619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6604 0.069 - 0.138: 2571 0.138 - 0.207: 599 0.207 - 0.275: 72 0.275 - 0.344: 108 Chirality restraints: 9954 Sorted by residual: chirality pdb=" C3' ADP C 601 " pdb=" C2' ADP C 601 " pdb=" C4' ADP C 601 " pdb=" O3' ADP C 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.85 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C3' ADP H 601 " pdb=" C2' ADP H 601 " pdb=" C4' ADP H 601 " pdb=" O3' ADP H 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.85 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C3' ADP F 601 " pdb=" C2' ADP F 601 " pdb=" C4' ADP F 601 " pdb=" O3' ADP F 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.85 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 9951 not shown) Planarity restraints: 10386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 26 " 0.085 2.00e-02 2.50e+03 4.45e-02 3.95e+01 pdb=" CG TYR E 26 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 26 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR E 26 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 26 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR E 26 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 26 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 26 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 26 " 0.085 2.00e-02 2.50e+03 4.44e-02 3.95e+01 pdb=" CG TYR D 26 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 26 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 26 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR D 26 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 26 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 26 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 26 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 26 " -0.085 2.00e-02 2.50e+03 4.44e-02 3.95e+01 pdb=" CG TYR I 26 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR I 26 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR I 26 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR I 26 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR I 26 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR I 26 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 26 " -0.061 2.00e-02 2.50e+03 ... (remaining 10383 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 12886 2.81 - 3.33: 60791 3.33 - 3.85: 89557 3.85 - 4.38: 98015 4.38 - 4.90: 163500 Nonbonded interactions: 424749 Sorted by model distance: nonbonded pdb=" OD1 ASP D 101 " pdb=" N GLY D 102 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP K 101 " pdb=" N GLY K 102 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP H 101 " pdb=" N GLY H 102 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP F 101 " pdb=" N GLY F 102 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP I 101 " pdb=" N GLY I 102 " model vdw 2.283 2.520 ... (remaining 424744 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.100 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: 0.050 Extract box with map and model: 18.480 Check model and map are aligned: 0.640 Set scattering table: 0.430 Process input model: 127.050 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.390 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.013 0.113 58968 Z= 0.878 Angle : 1.513 12.809 80172 Z= 0.898 Chirality : 0.079 0.344 9954 Planarity : 0.010 0.083 10386 Dihedral : 14.969 135.373 19926 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.08), residues: 8226 helix: -1.47 (0.06), residues: 4356 sheet: 0.37 (0.13), residues: 1170 loop : -0.55 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.008 TRP J 483 HIS 0.010 0.003 HIS H 476 PHE 0.006 0.003 PHE E 489 TYR 0.085 0.012 TYR I 26 ARG 0.044 0.006 ARG Q 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1310 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7754 (t80) cc_final: 0.7162 (t80) REVERT: A 69 ASN cc_start: 0.8836 (p0) cc_final: 0.8599 (p0) REVERT: A 90 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 91 ILE cc_start: 0.9192 (mt) cc_final: 0.8872 (mm) REVERT: A 104 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8503 (mtpt) REVERT: A 112 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 168 LEU cc_start: 0.9225 (tp) cc_final: 0.9023 (tp) REVERT: A 177 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8244 (mtm180) REVERT: A 471 GLN cc_start: 0.9175 (tt0) cc_final: 0.8802 (tm-30) REVERT: B 69 ASN cc_start: 0.8806 (p0) cc_final: 0.8570 (p0) REVERT: B 90 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8867 (tm-30) REVERT: B 91 ILE cc_start: 0.9086 (mt) cc_final: 0.8738 (mm) REVERT: B 104 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8432 (mtpt) REVERT: B 112 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 177 ARG cc_start: 0.8545 (mtt180) cc_final: 0.8182 (mtm180) REVERT: B 471 GLN cc_start: 0.9214 (tt0) cc_final: 0.9001 (tt0) REVERT: C 56 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8088 (mttt) REVERT: C 69 ASN cc_start: 0.8803 (p0) cc_final: 0.8542 (p0) REVERT: C 90 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8849 (tm-30) REVERT: C 91 ILE cc_start: 0.9149 (mt) cc_final: 0.8846 (mm) REVERT: C 104 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8460 (mtpt) REVERT: C 177 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8174 (mtm180) REVERT: C 526 ASP cc_start: 0.8489 (t0) cc_final: 0.6864 (t0) REVERT: D 69 ASN cc_start: 0.8788 (p0) cc_final: 0.8578 (p0) REVERT: D 78 MET cc_start: 0.8238 (mtp) cc_final: 0.8025 (mtp) REVERT: D 90 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8835 (tm-30) REVERT: D 91 ILE cc_start: 0.9195 (mt) cc_final: 0.8843 (mm) REVERT: D 104 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8500 (mtpt) REVERT: D 177 ARG cc_start: 0.8572 (mtt180) cc_final: 0.8209 (mtm180) REVERT: D 455 MET cc_start: 0.8697 (ttm) cc_final: 0.8479 (tmm) REVERT: D 471 GLN cc_start: 0.9162 (tt0) cc_final: 0.8946 (tt0) REVERT: E 49 TYR cc_start: 0.7780 (t80) cc_final: 0.7470 (t80) REVERT: E 54 MET cc_start: 0.8443 (pmm) cc_final: 0.8088 (ptm) REVERT: E 56 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8096 (mttt) REVERT: E 90 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8879 (tm-30) REVERT: E 91 ILE cc_start: 0.9138 (mt) cc_final: 0.8781 (mm) REVERT: E 104 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8353 (mtpt) REVERT: E 177 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8179 (mtm180) REVERT: E 471 GLN cc_start: 0.9138 (tt0) cc_final: 0.8903 (tt0) REVERT: F 69 ASN cc_start: 0.8791 (p0) cc_final: 0.8539 (p0) REVERT: F 90 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8933 (tm-30) REVERT: F 91 ILE cc_start: 0.9144 (mt) cc_final: 0.8876 (mm) REVERT: F 177 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8191 (mtm180) REVERT: F 471 GLN cc_start: 0.9183 (tt0) cc_final: 0.8968 (tt0) REVERT: F 526 ASP cc_start: 0.8412 (t0) cc_final: 0.6917 (t0) REVERT: G 49 TYR cc_start: 0.7812 (t80) cc_final: 0.7375 (t80) REVERT: G 69 ASN cc_start: 0.8861 (p0) cc_final: 0.8583 (p0) REVERT: G 90 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8894 (tm-30) REVERT: G 91 ILE cc_start: 0.9183 (mt) cc_final: 0.8882 (mm) REVERT: G 104 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8576 (mtpt) REVERT: G 108 ILE cc_start: 0.9336 (mm) cc_final: 0.9088 (tp) REVERT: G 112 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8306 (mm-30) REVERT: G 177 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8233 (mtm180) REVERT: G 471 GLN cc_start: 0.9163 (tt0) cc_final: 0.8943 (tt0) REVERT: H 69 ASN cc_start: 0.8868 (p0) cc_final: 0.8589 (p0) REVERT: H 90 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8787 (tm-30) REVERT: H 91 ILE cc_start: 0.9189 (mt) cc_final: 0.8845 (mm) REVERT: H 104 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8478 (mtpt) REVERT: H 177 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8175 (mtm180) REVERT: H 471 GLN cc_start: 0.9149 (tt0) cc_final: 0.8524 (tm-30) REVERT: H 526 ASP cc_start: 0.8349 (t0) cc_final: 0.7004 (t0) REVERT: I 90 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8909 (tm-30) REVERT: I 91 ILE cc_start: 0.9079 (mt) cc_final: 0.8795 (mm) REVERT: I 104 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8546 (mtpt) REVERT: I 177 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8139 (mtm180) REVERT: I 471 GLN cc_start: 0.9203 (tt0) cc_final: 0.8977 (tt0) REVERT: J 69 ASN cc_start: 0.8789 (p0) cc_final: 0.8579 (p0) REVERT: J 78 MET cc_start: 0.8236 (mtp) cc_final: 0.8031 (mtp) REVERT: J 90 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8837 (tm-30) REVERT: J 91 ILE cc_start: 0.9193 (mt) cc_final: 0.8844 (mm) REVERT: J 104 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8509 (mtpt) REVERT: J 177 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8211 (mtm180) REVERT: J 455 MET cc_start: 0.8696 (ttm) cc_final: 0.8477 (tmm) REVERT: J 471 GLN cc_start: 0.9161 (tt0) cc_final: 0.8946 (tt0) REVERT: K 49 TYR cc_start: 0.7776 (t80) cc_final: 0.7467 (t80) REVERT: K 54 MET cc_start: 0.8438 (pmm) cc_final: 0.8087 (ptm) REVERT: K 56 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8097 (mttt) REVERT: K 90 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8880 (tm-30) REVERT: K 91 ILE cc_start: 0.9139 (mt) cc_final: 0.8783 (mm) REVERT: K 104 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8358 (mtpt) REVERT: K 177 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8182 (mtm180) REVERT: K 471 GLN cc_start: 0.9141 (tt0) cc_final: 0.8906 (tt0) REVERT: L 69 ASN cc_start: 0.8790 (p0) cc_final: 0.8537 (p0) REVERT: L 90 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8933 (tm-30) REVERT: L 91 ILE cc_start: 0.9145 (mt) cc_final: 0.8877 (mm) REVERT: L 177 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8190 (mtm180) REVERT: L 471 GLN cc_start: 0.9184 (tt0) cc_final: 0.8968 (tt0) REVERT: L 526 ASP cc_start: 0.8414 (t0) cc_final: 0.6922 (t0) REVERT: M 49 TYR cc_start: 0.7814 (t80) cc_final: 0.7371 (t80) REVERT: M 69 ASN cc_start: 0.8870 (p0) cc_final: 0.8594 (p0) REVERT: M 90 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8895 (tm-30) REVERT: M 91 ILE cc_start: 0.9182 (mt) cc_final: 0.8881 (mm) REVERT: M 104 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8583 (mtpt) REVERT: M 108 ILE cc_start: 0.9335 (mm) cc_final: 0.9090 (tp) REVERT: M 112 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8304 (mm-30) REVERT: M 177 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8233 (mtm180) REVERT: M 471 GLN cc_start: 0.9161 (tt0) cc_final: 0.8944 (tt0) REVERT: N 69 ASN cc_start: 0.8864 (p0) cc_final: 0.8588 (p0) REVERT: N 90 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8785 (tm-30) REVERT: N 91 ILE cc_start: 0.9188 (mt) cc_final: 0.8845 (mm) REVERT: N 104 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8479 (mtpt) REVERT: N 177 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8173 (mtm180) REVERT: N 471 GLN cc_start: 0.9151 (tt0) cc_final: 0.8529 (tm-30) REVERT: N 526 ASP cc_start: 0.8353 (t0) cc_final: 0.7006 (t0) REVERT: O 90 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8910 (tm-30) REVERT: O 91 ILE cc_start: 0.9077 (mt) cc_final: 0.8795 (mm) REVERT: O 104 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8548 (mtpt) REVERT: O 177 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8134 (mtm180) REVERT: O 471 GLN cc_start: 0.9202 (tt0) cc_final: 0.8976 (tt0) REVERT: P 49 TYR cc_start: 0.7761 (t80) cc_final: 0.7166 (t80) REVERT: P 69 ASN cc_start: 0.8839 (p0) cc_final: 0.8604 (p0) REVERT: P 90 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8841 (tm-30) REVERT: P 91 ILE cc_start: 0.9192 (mt) cc_final: 0.8869 (mm) REVERT: P 104 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8503 (mtpt) REVERT: P 112 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8304 (mm-30) REVERT: P 168 LEU cc_start: 0.9224 (tp) cc_final: 0.9022 (tp) REVERT: P 177 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8245 (mtm180) REVERT: P 471 GLN cc_start: 0.9176 (tt0) cc_final: 0.8801 (tm-30) REVERT: Q 69 ASN cc_start: 0.8807 (p0) cc_final: 0.8575 (p0) REVERT: Q 90 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8867 (tm-30) REVERT: Q 91 ILE cc_start: 0.9088 (mt) cc_final: 0.8737 (mm) REVERT: Q 104 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8432 (mtpt) REVERT: Q 112 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8389 (mm-30) REVERT: Q 177 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8185 (mtm180) REVERT: Q 471 GLN cc_start: 0.9217 (tt0) cc_final: 0.9002 (tt0) REVERT: R 69 ASN cc_start: 0.8799 (p0) cc_final: 0.8533 (p0) REVERT: R 90 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8847 (tm-30) REVERT: R 91 ILE cc_start: 0.9148 (mt) cc_final: 0.8842 (mm) REVERT: R 104 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8462 (mtpt) REVERT: R 177 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8168 (mtm180) REVERT: R 526 ASP cc_start: 0.8491 (t0) cc_final: 0.6862 (t0) outliers start: 0 outliers final: 0 residues processed: 1310 average time/residue: 0.5797 time to fit residues: 1256.6125 Evaluate side-chains 739 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 739 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 714 optimal weight: 0.9990 chunk 641 optimal weight: 50.0000 chunk 355 optimal weight: 0.5980 chunk 219 optimal weight: 50.0000 chunk 432 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 chunk 663 optimal weight: 0.7980 chunk 256 optimal weight: 0.8980 chunk 403 optimal weight: 50.0000 chunk 493 optimal weight: 0.0270 chunk 768 optimal weight: 6.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 126 HIS B 95 GLN B 126 HIS B 434 GLN C 95 GLN C 126 HIS D 95 GLN D 126 HIS E 95 GLN E 126 HIS E 434 GLN F 126 HIS G 95 GLN G 126 HIS H 95 GLN H 126 HIS I 95 GLN I 126 HIS J 95 GLN J 126 HIS K 95 GLN K 126 HIS K 434 GLN L 126 HIS M 95 GLN M 126 HIS ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 HIS O 95 GLN O 126 HIS P 95 GLN P 126 HIS Q 95 GLN Q 126 HIS Q 434 GLN R 95 GLN R 126 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 58968 Z= 0.153 Angle : 0.621 6.479 80172 Z= 0.320 Chirality : 0.042 0.191 9954 Planarity : 0.004 0.042 10386 Dihedral : 8.184 111.253 9000 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.10 % Allowed : 1.31 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.23 (0.09), residues: 8226 helix: 0.44 (0.08), residues: 4410 sheet: 0.87 (0.14), residues: 1170 loop : -0.46 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 483 HIS 0.008 0.001 HIS Q 126 PHE 0.002 0.000 PHE C 489 TYR 0.013 0.002 TYR G 179 ARG 0.004 0.000 ARG G 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1098 time to evaluate : 5.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7442 (t80) cc_final: 0.6956 (t80) REVERT: A 54 MET cc_start: 0.8564 (ptm) cc_final: 0.7711 (ptm) REVERT: A 90 GLN cc_start: 0.9305 (tm-30) cc_final: 0.9025 (tm-30) REVERT: A 95 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7224 (tp-100) REVERT: A 104 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8289 (mtpt) REVERT: A 108 ILE cc_start: 0.9281 (mm) cc_final: 0.9067 (tp) REVERT: A 404 VAL cc_start: 0.9197 (t) cc_final: 0.8908 (p) REVERT: A 423 GLU cc_start: 0.8741 (tt0) cc_final: 0.8252 (mm-30) REVERT: A 455 MET cc_start: 0.8403 (tmm) cc_final: 0.8188 (tmm) REVERT: A 487 ASN cc_start: 0.7025 (t0) cc_final: 0.6659 (t0) REVERT: B 54 MET cc_start: 0.8567 (ptm) cc_final: 0.7803 (ptt) REVERT: B 90 GLN cc_start: 0.9231 (tm-30) cc_final: 0.9005 (tm-30) REVERT: B 104 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8314 (mtpt) REVERT: B 126 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8241 (t70) REVERT: B 404 VAL cc_start: 0.9149 (t) cc_final: 0.8858 (p) REVERT: B 455 MET cc_start: 0.8441 (tmm) cc_final: 0.8188 (tmm) REVERT: B 460 ASN cc_start: 0.7880 (m-40) cc_final: 0.7664 (m-40) REVERT: B 471 GLN cc_start: 0.9224 (tt0) cc_final: 0.8987 (tt0) REVERT: B 487 ASN cc_start: 0.7277 (t0) cc_final: 0.6746 (t0) REVERT: B 494 GLU cc_start: 0.7377 (mp0) cc_final: 0.7132 (mp0) REVERT: B 526 ASP cc_start: 0.8212 (t0) cc_final: 0.7285 (t0) REVERT: C 54 MET cc_start: 0.8470 (ptm) cc_final: 0.7880 (ptm) REVERT: C 69 ASN cc_start: 0.8662 (p0) cc_final: 0.8296 (p0) REVERT: C 90 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8987 (tm-30) REVERT: C 104 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8340 (mtpt) REVERT: C 455 MET cc_start: 0.8307 (tmm) cc_final: 0.7935 (tmm) REVERT: C 484 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: C 487 ASN cc_start: 0.7352 (t0) cc_final: 0.6776 (t0) REVERT: C 494 GLU cc_start: 0.7323 (mp0) cc_final: 0.7108 (mp0) REVERT: C 526 ASP cc_start: 0.8449 (t0) cc_final: 0.7843 (t0) REVERT: D 90 GLN cc_start: 0.9299 (tm-30) cc_final: 0.9039 (tm-30) REVERT: D 134 TYR cc_start: 0.9093 (m-10) cc_final: 0.8777 (m-80) REVERT: D 404 VAL cc_start: 0.9146 (t) cc_final: 0.8878 (p) REVERT: D 423 GLU cc_start: 0.8863 (tt0) cc_final: 0.8618 (mm-30) REVERT: D 471 GLN cc_start: 0.9141 (tt0) cc_final: 0.8905 (tt0) REVERT: D 487 ASN cc_start: 0.7085 (t0) cc_final: 0.6532 (t0) REVERT: D 526 ASP cc_start: 0.8271 (t0) cc_final: 0.6815 (t0) REVERT: E 49 TYR cc_start: 0.7619 (t80) cc_final: 0.7312 (t80) REVERT: E 55 ASP cc_start: 0.8407 (m-30) cc_final: 0.8196 (m-30) REVERT: E 90 GLN cc_start: 0.9254 (tm-30) cc_final: 0.9027 (tm-30) REVERT: E 104 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8281 (mtpt) REVERT: E 108 ILE cc_start: 0.9349 (mm) cc_final: 0.9131 (tp) REVERT: E 150 GLN cc_start: 0.9178 (mm110) cc_final: 0.8975 (mm110) REVERT: E 404 VAL cc_start: 0.9168 (t) cc_final: 0.8899 (p) REVERT: E 455 MET cc_start: 0.8396 (tmm) cc_final: 0.8086 (tmm) REVERT: E 471 GLN cc_start: 0.9153 (tt0) cc_final: 0.8866 (tt0) REVERT: E 487 ASN cc_start: 0.7301 (t0) cc_final: 0.6843 (t0) REVERT: E 494 GLU cc_start: 0.7375 (mp0) cc_final: 0.6871 (mp0) REVERT: F 54 MET cc_start: 0.8463 (ptm) cc_final: 0.7909 (ptm) REVERT: F 90 GLN cc_start: 0.9239 (tm-30) cc_final: 0.9004 (tm-30) REVERT: F 404 VAL cc_start: 0.9200 (t) cc_final: 0.8936 (p) REVERT: F 423 GLU cc_start: 0.8691 (tt0) cc_final: 0.8432 (mm-30) REVERT: F 455 MET cc_start: 0.8506 (tmm) cc_final: 0.8189 (tmm) REVERT: F 487 ASN cc_start: 0.7249 (t0) cc_final: 0.6754 (t0) REVERT: F 521 LEU cc_start: 0.9173 (mm) cc_final: 0.8971 (tt) REVERT: G 49 TYR cc_start: 0.7551 (t80) cc_final: 0.7216 (t80) REVERT: G 54 MET cc_start: 0.8599 (ptm) cc_final: 0.7909 (ptm) REVERT: G 69 ASN cc_start: 0.8664 (p0) cc_final: 0.8413 (p0) REVERT: G 90 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9019 (tm-30) REVERT: G 104 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8189 (mtmt) REVERT: G 108 ILE cc_start: 0.9287 (mm) cc_final: 0.9071 (tp) REVERT: G 404 VAL cc_start: 0.9114 (t) cc_final: 0.8848 (p) REVERT: G 455 MET cc_start: 0.8501 (tmm) cc_final: 0.8267 (tmm) REVERT: G 471 GLN cc_start: 0.9163 (tt0) cc_final: 0.8877 (tt0) REVERT: G 487 ASN cc_start: 0.7267 (t0) cc_final: 0.6829 (t0) REVERT: G 526 ASP cc_start: 0.8263 (t0) cc_final: 0.6717 (t0) REVERT: H 90 GLN cc_start: 0.9300 (tm-30) cc_final: 0.9026 (tm-30) REVERT: H 212 HIS cc_start: 0.7952 (m90) cc_final: 0.7573 (m90) REVERT: H 404 VAL cc_start: 0.9129 (t) cc_final: 0.8858 (p) REVERT: H 455 MET cc_start: 0.8471 (tmm) cc_final: 0.8065 (tmm) REVERT: H 471 GLN cc_start: 0.9189 (tt0) cc_final: 0.8835 (tm-30) REVERT: H 484 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: H 487 ASN cc_start: 0.7032 (t0) cc_final: 0.6593 (t0) REVERT: H 494 GLU cc_start: 0.7482 (mp0) cc_final: 0.7107 (mp0) REVERT: H 526 ASP cc_start: 0.8310 (t0) cc_final: 0.6726 (t0) REVERT: I 55 ASP cc_start: 0.8294 (m-30) cc_final: 0.8004 (m-30) REVERT: I 90 GLN cc_start: 0.9301 (tm-30) cc_final: 0.9028 (tm-30) REVERT: I 150 GLN cc_start: 0.9090 (mm110) cc_final: 0.8873 (mm110) REVERT: I 404 VAL cc_start: 0.9147 (t) cc_final: 0.8866 (p) REVERT: I 455 MET cc_start: 0.8468 (tmm) cc_final: 0.8240 (tmm) REVERT: I 471 GLN cc_start: 0.9173 (tt0) cc_final: 0.8894 (tt0) REVERT: I 483 TRP cc_start: 0.8483 (m100) cc_final: 0.7462 (m-10) REVERT: I 487 ASN cc_start: 0.7408 (t0) cc_final: 0.6913 (t0) REVERT: I 494 GLU cc_start: 0.7352 (mp0) cc_final: 0.6814 (mp0) REVERT: I 521 LEU cc_start: 0.9171 (mm) cc_final: 0.8927 (tt) REVERT: J 90 GLN cc_start: 0.9300 (tm-30) cc_final: 0.9038 (tm-30) REVERT: J 134 TYR cc_start: 0.9089 (m-10) cc_final: 0.8775 (m-80) REVERT: J 404 VAL cc_start: 0.9146 (t) cc_final: 0.8879 (p) REVERT: J 423 GLU cc_start: 0.8864 (tt0) cc_final: 0.8621 (mm-30) REVERT: J 471 GLN cc_start: 0.9143 (tt0) cc_final: 0.8904 (tt0) REVERT: J 487 ASN cc_start: 0.7079 (t0) cc_final: 0.6528 (t0) REVERT: K 49 TYR cc_start: 0.7615 (t80) cc_final: 0.7302 (t80) REVERT: K 55 ASP cc_start: 0.8412 (m-30) cc_final: 0.8204 (m-30) REVERT: K 90 GLN cc_start: 0.9254 (tm-30) cc_final: 0.9027 (tm-30) REVERT: K 104 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8289 (mtpt) REVERT: K 108 ILE cc_start: 0.9348 (mm) cc_final: 0.9135 (tp) REVERT: K 150 GLN cc_start: 0.9176 (mm110) cc_final: 0.8971 (mm110) REVERT: K 404 VAL cc_start: 0.9170 (t) cc_final: 0.8900 (p) REVERT: K 455 MET cc_start: 0.8394 (tmm) cc_final: 0.8080 (tmm) REVERT: K 471 GLN cc_start: 0.9154 (tt0) cc_final: 0.8870 (tt0) REVERT: K 487 ASN cc_start: 0.7300 (t0) cc_final: 0.6845 (t0) REVERT: K 494 GLU cc_start: 0.7378 (mp0) cc_final: 0.6873 (mp0) REVERT: L 54 MET cc_start: 0.8470 (ptm) cc_final: 0.7916 (ptm) REVERT: L 90 GLN cc_start: 0.9239 (tm-30) cc_final: 0.9004 (tm-30) REVERT: L 404 VAL cc_start: 0.9203 (t) cc_final: 0.8942 (p) REVERT: L 423 GLU cc_start: 0.8677 (tt0) cc_final: 0.8430 (mm-30) REVERT: L 455 MET cc_start: 0.8498 (tmm) cc_final: 0.8183 (tmm) REVERT: L 471 GLN cc_start: 0.9178 (tt0) cc_final: 0.8976 (tt0) REVERT: L 487 ASN cc_start: 0.7240 (t0) cc_final: 0.6754 (t0) REVERT: L 521 LEU cc_start: 0.9171 (mm) cc_final: 0.8962 (tt) REVERT: M 49 TYR cc_start: 0.7558 (t80) cc_final: 0.7221 (t80) REVERT: M 54 MET cc_start: 0.8593 (ptm) cc_final: 0.7905 (ptm) REVERT: M 69 ASN cc_start: 0.8663 (p0) cc_final: 0.8413 (p0) REVERT: M 90 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9017 (tm-30) REVERT: M 104 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8192 (mtmt) REVERT: M 108 ILE cc_start: 0.9287 (mm) cc_final: 0.9073 (tp) REVERT: M 404 VAL cc_start: 0.9111 (t) cc_final: 0.8847 (p) REVERT: M 455 MET cc_start: 0.8500 (tmm) cc_final: 0.8257 (tmm) REVERT: M 471 GLN cc_start: 0.9164 (tt0) cc_final: 0.8878 (tt0) REVERT: M 487 ASN cc_start: 0.7260 (t0) cc_final: 0.6823 (t0) REVERT: M 526 ASP cc_start: 0.8255 (t0) cc_final: 0.6718 (t0) REVERT: N 54 MET cc_start: 0.8614 (ptm) cc_final: 0.7815 (ptm) REVERT: N 90 GLN cc_start: 0.9299 (tm-30) cc_final: 0.9027 (tm-30) REVERT: N 212 HIS cc_start: 0.7958 (m90) cc_final: 0.7581 (m90) REVERT: N 404 VAL cc_start: 0.9132 (t) cc_final: 0.8862 (p) REVERT: N 455 MET cc_start: 0.8457 (tmm) cc_final: 0.8051 (tmm) REVERT: N 471 GLN cc_start: 0.9189 (tt0) cc_final: 0.8835 (tm-30) REVERT: N 484 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: N 487 ASN cc_start: 0.7031 (t0) cc_final: 0.6596 (t0) REVERT: N 494 GLU cc_start: 0.7481 (mp0) cc_final: 0.7105 (mp0) REVERT: N 526 ASP cc_start: 0.8309 (t0) cc_final: 0.6732 (t0) REVERT: O 90 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9026 (tm-30) REVERT: O 104 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8352 (mtpt) REVERT: O 150 GLN cc_start: 0.9102 (mm110) cc_final: 0.8881 (mm110) REVERT: O 404 VAL cc_start: 0.9146 (t) cc_final: 0.8864 (p) REVERT: O 444 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8604 (tm-30) REVERT: O 455 MET cc_start: 0.8462 (tmm) cc_final: 0.8231 (tmm) REVERT: O 471 GLN cc_start: 0.9171 (tt0) cc_final: 0.8897 (tt0) REVERT: O 483 TRP cc_start: 0.8483 (m100) cc_final: 0.7461 (m-10) REVERT: O 487 ASN cc_start: 0.7415 (t0) cc_final: 0.6917 (t0) REVERT: O 494 GLU cc_start: 0.7343 (mp0) cc_final: 0.6806 (mp0) REVERT: O 521 LEU cc_start: 0.9166 (mm) cc_final: 0.8935 (tt) REVERT: O 526 ASP cc_start: 0.8256 (t0) cc_final: 0.6582 (t0) REVERT: P 49 TYR cc_start: 0.7450 (t80) cc_final: 0.6956 (t80) REVERT: P 54 MET cc_start: 0.8560 (ptm) cc_final: 0.7705 (ptm) REVERT: P 90 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9021 (tm-30) REVERT: P 95 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7216 (tp-100) REVERT: P 104 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8292 (mtpt) REVERT: P 108 ILE cc_start: 0.9279 (mm) cc_final: 0.9067 (tp) REVERT: P 404 VAL cc_start: 0.9198 (t) cc_final: 0.8908 (p) REVERT: P 423 GLU cc_start: 0.8741 (tt0) cc_final: 0.8252 (mm-30) REVERT: P 455 MET cc_start: 0.8398 (tmm) cc_final: 0.8187 (tmm) REVERT: P 487 ASN cc_start: 0.7025 (t0) cc_final: 0.6663 (t0) REVERT: Q 54 MET cc_start: 0.8565 (ptm) cc_final: 0.7798 (ptt) REVERT: Q 90 GLN cc_start: 0.9233 (tm-30) cc_final: 0.9005 (tm-30) REVERT: Q 104 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8317 (mtpt) REVERT: Q 404 VAL cc_start: 0.9152 (t) cc_final: 0.8859 (p) REVERT: Q 455 MET cc_start: 0.8438 (tmm) cc_final: 0.8190 (tmm) REVERT: Q 460 ASN cc_start: 0.7878 (m-40) cc_final: 0.7665 (m-40) REVERT: Q 471 GLN cc_start: 0.9226 (tt0) cc_final: 0.8990 (tt0) REVERT: Q 487 ASN cc_start: 0.7283 (t0) cc_final: 0.6741 (t0) REVERT: Q 494 GLU cc_start: 0.7378 (mp0) cc_final: 0.7132 (mp0) REVERT: Q 526 ASP cc_start: 0.8212 (t0) cc_final: 0.7282 (t0) REVERT: R 69 ASN cc_start: 0.8646 (p0) cc_final: 0.8293 (p0) REVERT: R 90 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8986 (tm-30) REVERT: R 104 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8330 (mtpt) REVERT: R 455 MET cc_start: 0.8318 (tmm) cc_final: 0.7932 (tmm) REVERT: R 484 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: R 487 ASN cc_start: 0.7350 (t0) cc_final: 0.6777 (t0) REVERT: R 494 GLU cc_start: 0.7322 (mp0) cc_final: 0.7114 (mp0) REVERT: R 526 ASP cc_start: 0.8446 (t0) cc_final: 0.7845 (t0) outliers start: 53 outliers final: 8 residues processed: 1147 average time/residue: 0.5368 time to fit residues: 1077.0482 Evaluate side-chains 831 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 816 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 426 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 639 optimal weight: 50.0000 chunk 523 optimal weight: 6.9990 chunk 211 optimal weight: 0.1980 chunk 769 optimal weight: 10.0000 chunk 831 optimal weight: 50.0000 chunk 685 optimal weight: 40.0000 chunk 763 optimal weight: 0.7980 chunk 262 optimal weight: 30.0000 chunk 617 optimal weight: 2.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS C 95 GLN C 126 HIS D 126 HIS E 95 GLN E 126 HIS F 126 HIS G 126 HIS H 95 GLN H 126 HIS I 95 GLN I 126 HIS J 126 HIS K 95 GLN K 126 HIS L 126 HIS M 126 HIS N 95 GLN N 126 HIS O 95 GLN O 126 HIS P 126 HIS Q 126 HIS R 95 GLN R 126 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 58968 Z= 0.332 Angle : 0.695 7.227 80172 Z= 0.355 Chirality : 0.044 0.174 9954 Planarity : 0.004 0.045 10386 Dihedral : 6.794 90.262 9000 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.32 (0.09), residues: 8226 helix: 0.59 (0.08), residues: 4392 sheet: 0.95 (0.14), residues: 1188 loop : -0.60 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 483 HIS 0.002 0.001 HIS R 82 PHE 0.003 0.001 PHE P 489 TYR 0.024 0.002 TYR L 431 ARG 0.005 0.001 ARG E 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 862 time to evaluate : 5.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.8126 (t80) cc_final: 0.7634 (t80) REVERT: A 90 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 455 MET cc_start: 0.8511 (tmm) cc_final: 0.8310 (tmm) REVERT: A 487 ASN cc_start: 0.7692 (t0) cc_final: 0.6561 (t0) REVERT: A 494 GLU cc_start: 0.7554 (mp0) cc_final: 0.7285 (mp0) REVERT: B 54 MET cc_start: 0.8691 (ptm) cc_final: 0.7771 (ptm) REVERT: B 90 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8988 (tm-30) REVERT: B 455 MET cc_start: 0.8442 (tmm) cc_final: 0.8232 (tmm) REVERT: B 471 GLN cc_start: 0.9255 (tt0) cc_final: 0.9047 (tt0) REVERT: B 482 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8539 (tptt) REVERT: C 49 TYR cc_start: 0.7952 (t80) cc_final: 0.7739 (t80) REVERT: C 54 MET cc_start: 0.8698 (ptm) cc_final: 0.7914 (ptm) REVERT: C 90 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8964 (tm-30) REVERT: C 177 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8073 (mtt90) REVERT: C 455 MET cc_start: 0.8504 (tmm) cc_final: 0.8094 (tmm) REVERT: C 487 ASN cc_start: 0.7707 (t0) cc_final: 0.6482 (t0) REVERT: C 526 ASP cc_start: 0.8675 (t0) cc_final: 0.8058 (t0) REVERT: D 42 GLU cc_start: 0.8593 (pp20) cc_final: 0.8240 (tt0) REVERT: D 90 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8999 (tm-30) REVERT: D 455 MET cc_start: 0.8467 (tmm) cc_final: 0.8246 (tmm) REVERT: D 471 GLN cc_start: 0.9192 (tt0) cc_final: 0.8965 (tt0) REVERT: D 526 ASP cc_start: 0.8709 (t0) cc_final: 0.7694 (t70) REVERT: E 49 TYR cc_start: 0.8117 (t80) cc_final: 0.7781 (t80) REVERT: E 90 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9000 (tm-30) REVERT: E 201 VAL cc_start: 0.8930 (t) cc_final: 0.8693 (t) REVERT: E 391 ASP cc_start: 0.8734 (t0) cc_final: 0.8523 (m-30) REVERT: E 404 VAL cc_start: 0.9272 (t) cc_final: 0.9042 (p) REVERT: E 455 MET cc_start: 0.8562 (tmm) cc_final: 0.8202 (tmm) REVERT: E 471 GLN cc_start: 0.9231 (tt0) cc_final: 0.9014 (tt0) REVERT: E 487 ASN cc_start: 0.7642 (t0) cc_final: 0.6367 (t0) REVERT: E 494 GLU cc_start: 0.7591 (mp0) cc_final: 0.7360 (mp0) REVERT: E 496 MET cc_start: 0.7775 (mmp) cc_final: 0.7570 (mmm) REVERT: E 526 ASP cc_start: 0.8703 (t0) cc_final: 0.8351 (t0) REVERT: F 54 MET cc_start: 0.8734 (ptm) cc_final: 0.8088 (ptm) REVERT: F 90 GLN cc_start: 0.9275 (tm-30) cc_final: 0.9030 (tm-30) REVERT: F 455 MET cc_start: 0.8518 (tmm) cc_final: 0.8195 (tmm) REVERT: F 487 ASN cc_start: 0.7598 (t0) cc_final: 0.7196 (t0) REVERT: G 49 TYR cc_start: 0.8037 (t80) cc_final: 0.7570 (t80) REVERT: G 54 MET cc_start: 0.8626 (ptm) cc_final: 0.8029 (ptm) REVERT: G 90 GLN cc_start: 0.9288 (tm-30) cc_final: 0.9001 (tm-30) REVERT: G 391 ASP cc_start: 0.8873 (t0) cc_final: 0.8622 (m-30) REVERT: G 455 MET cc_start: 0.8623 (tmm) cc_final: 0.8335 (tmm) REVERT: G 521 LEU cc_start: 0.9252 (tp) cc_final: 0.8931 (tt) REVERT: G 526 ASP cc_start: 0.8571 (t0) cc_final: 0.7519 (t70) REVERT: H 90 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8947 (tm-30) REVERT: H 455 MET cc_start: 0.8506 (tmm) cc_final: 0.8236 (tmm) REVERT: H 487 ASN cc_start: 0.7891 (t0) cc_final: 0.6686 (t0) REVERT: H 496 MET cc_start: 0.7787 (mmp) cc_final: 0.7558 (mmm) REVERT: H 526 ASP cc_start: 0.8657 (t0) cc_final: 0.7689 (t70) REVERT: I 54 MET cc_start: 0.9136 (pmm) cc_final: 0.8935 (ptp) REVERT: I 55 ASP cc_start: 0.8423 (m-30) cc_final: 0.8187 (m-30) REVERT: I 90 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9011 (tm-30) REVERT: I 455 MET cc_start: 0.8606 (tmm) cc_final: 0.8229 (tmm) REVERT: I 487 ASN cc_start: 0.7649 (t0) cc_final: 0.6239 (t0) REVERT: I 496 MET cc_start: 0.7707 (mmp) cc_final: 0.7499 (mmm) REVERT: J 42 GLU cc_start: 0.8590 (pp20) cc_final: 0.8234 (tt0) REVERT: J 90 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8999 (tm-30) REVERT: J 455 MET cc_start: 0.8462 (tmm) cc_final: 0.8247 (tmm) REVERT: J 471 GLN cc_start: 0.9194 (tt0) cc_final: 0.8965 (tt0) REVERT: K 49 TYR cc_start: 0.8112 (t80) cc_final: 0.7777 (t80) REVERT: K 90 GLN cc_start: 0.9298 (tm-30) cc_final: 0.9000 (tm-30) REVERT: K 201 VAL cc_start: 0.8932 (t) cc_final: 0.8693 (t) REVERT: K 391 ASP cc_start: 0.8733 (t0) cc_final: 0.8524 (m-30) REVERT: K 404 VAL cc_start: 0.9272 (t) cc_final: 0.9044 (p) REVERT: K 455 MET cc_start: 0.8556 (tmm) cc_final: 0.8204 (tmm) REVERT: K 471 GLN cc_start: 0.9234 (tt0) cc_final: 0.9017 (tt0) REVERT: K 487 ASN cc_start: 0.7640 (t0) cc_final: 0.6367 (t0) REVERT: K 494 GLU cc_start: 0.7583 (mp0) cc_final: 0.7354 (mp0) REVERT: K 496 MET cc_start: 0.7783 (mmp) cc_final: 0.7566 (mmm) REVERT: K 526 ASP cc_start: 0.8702 (t0) cc_final: 0.8298 (t0) REVERT: L 54 MET cc_start: 0.8738 (ptm) cc_final: 0.8089 (ptm) REVERT: L 90 GLN cc_start: 0.9274 (tm-30) cc_final: 0.9030 (tm-30) REVERT: L 177 ARG cc_start: 0.8233 (mtt180) cc_final: 0.8031 (mtt90) REVERT: L 455 MET cc_start: 0.8513 (tmm) cc_final: 0.8191 (tmm) REVERT: L 487 ASN cc_start: 0.7587 (t0) cc_final: 0.7162 (t0) REVERT: M 49 TYR cc_start: 0.8041 (t80) cc_final: 0.7576 (t80) REVERT: M 54 MET cc_start: 0.8624 (ptm) cc_final: 0.8019 (ptm) REVERT: M 90 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9004 (tm-30) REVERT: M 391 ASP cc_start: 0.8845 (t0) cc_final: 0.8596 (m-30) REVERT: M 455 MET cc_start: 0.8623 (tmm) cc_final: 0.8339 (tmm) REVERT: M 521 LEU cc_start: 0.9255 (tp) cc_final: 0.8935 (tt) REVERT: M 526 ASP cc_start: 0.8568 (t0) cc_final: 0.7520 (t70) REVERT: N 54 MET cc_start: 0.8738 (ptm) cc_final: 0.7661 (ptm) REVERT: N 90 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8960 (tm-30) REVERT: N 455 MET cc_start: 0.8501 (tmm) cc_final: 0.8231 (tmm) REVERT: N 487 ASN cc_start: 0.7887 (t0) cc_final: 0.6684 (t0) REVERT: N 496 MET cc_start: 0.7790 (mmp) cc_final: 0.7561 (mmm) REVERT: N 526 ASP cc_start: 0.8654 (t0) cc_final: 0.7675 (t70) REVERT: O 90 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9016 (tm-30) REVERT: O 455 MET cc_start: 0.8555 (tmm) cc_final: 0.8176 (tmm) REVERT: O 487 ASN cc_start: 0.7661 (t0) cc_final: 0.6237 (t0) REVERT: O 496 MET cc_start: 0.7721 (mmp) cc_final: 0.7513 (mmm) REVERT: O 526 ASP cc_start: 0.8751 (t0) cc_final: 0.7474 (t0) REVERT: P 49 TYR cc_start: 0.8128 (t80) cc_final: 0.7628 (t80) REVERT: P 90 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8936 (tm-30) REVERT: P 455 MET cc_start: 0.8509 (tmm) cc_final: 0.8308 (tmm) REVERT: P 487 ASN cc_start: 0.7697 (t0) cc_final: 0.6561 (t0) REVERT: P 494 GLU cc_start: 0.7550 (mp0) cc_final: 0.7288 (mp0) REVERT: Q 54 MET cc_start: 0.8689 (ptm) cc_final: 0.7769 (ptm) REVERT: Q 90 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8986 (tm-30) REVERT: Q 455 MET cc_start: 0.8438 (tmm) cc_final: 0.8231 (tmm) REVERT: Q 471 GLN cc_start: 0.9257 (tt0) cc_final: 0.9042 (tt0) REVERT: Q 482 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8517 (tptt) REVERT: R 90 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8966 (tm-30) REVERT: R 177 ARG cc_start: 0.8327 (mtt180) cc_final: 0.8076 (mtt90) REVERT: R 455 MET cc_start: 0.8497 (tmm) cc_final: 0.8096 (tmm) REVERT: R 487 ASN cc_start: 0.7810 (t0) cc_final: 0.6601 (t0) REVERT: R 526 ASP cc_start: 0.8667 (t0) cc_final: 0.8057 (t0) outliers start: 5 outliers final: 2 residues processed: 864 average time/residue: 0.5331 time to fit residues: 780.5657 Evaluate side-chains 624 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 622 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 760 optimal weight: 0.9980 chunk 578 optimal weight: 9.9990 chunk 399 optimal weight: 40.0000 chunk 85 optimal weight: 0.9990 chunk 367 optimal weight: 0.7980 chunk 516 optimal weight: 0.9990 chunk 772 optimal weight: 30.0000 chunk 817 optimal weight: 20.0000 chunk 403 optimal weight: 50.0000 chunk 732 optimal weight: 50.0000 chunk 220 optimal weight: 50.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN B 95 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN F 95 GLN F 126 HIS F 460 ASN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 126 HIS H 460 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS I 460 ASN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS K 460 ASN L 95 GLN L 126 HIS L 460 ASN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN N 126 HIS N 460 ASN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS P 95 GLN P 126 HIS P 460 ASN Q 95 GLN ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 460 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 58968 Z= 0.262 Angle : 0.623 8.458 80172 Z= 0.318 Chirality : 0.043 0.163 9954 Planarity : 0.004 0.043 10386 Dihedral : 6.207 78.346 9000 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.41 (0.09), residues: 8226 helix: 0.66 (0.08), residues: 4392 sheet: 0.96 (0.15), residues: 1188 loop : -0.56 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 483 HIS 0.003 0.001 HIS N 212 PHE 0.003 0.001 PHE N 489 TYR 0.014 0.002 TYR F 431 ARG 0.005 0.001 ARG M 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 794 time to evaluate : 5.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.8062 (t80) cc_final: 0.7736 (t80) REVERT: B 54 MET cc_start: 0.8663 (ptm) cc_final: 0.7603 (ptm) REVERT: B 55 ASP cc_start: 0.8601 (m-30) cc_final: 0.8250 (m-30) REVERT: B 90 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8956 (tm-30) REVERT: B 455 MET cc_start: 0.8418 (tmm) cc_final: 0.8208 (tmm) REVERT: B 526 ASP cc_start: 0.8595 (t0) cc_final: 0.7929 (t0) REVERT: C 54 MET cc_start: 0.8689 (ptm) cc_final: 0.7711 (ptm) REVERT: C 90 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8952 (tm-30) REVERT: C 104 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8385 (mtmt) REVERT: C 177 ARG cc_start: 0.8280 (mtt180) cc_final: 0.8063 (mtt90) REVERT: C 455 MET cc_start: 0.8418 (tmm) cc_final: 0.8119 (tmm) REVERT: C 526 ASP cc_start: 0.8692 (t0) cc_final: 0.7788 (t0) REVERT: D 90 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8956 (tm-30) REVERT: D 526 ASP cc_start: 0.8624 (t0) cc_final: 0.7297 (t0) REVERT: E 49 TYR cc_start: 0.8184 (t80) cc_final: 0.7888 (t80) REVERT: E 90 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8994 (tm-30) REVERT: E 150 GLN cc_start: 0.9210 (mm110) cc_final: 0.8840 (mm110) REVERT: E 455 MET cc_start: 0.8539 (tmm) cc_final: 0.8125 (tmm) REVERT: E 471 GLN cc_start: 0.9225 (tt0) cc_final: 0.8977 (tt0) REVERT: E 494 GLU cc_start: 0.7621 (mp0) cc_final: 0.7371 (mp0) REVERT: E 526 ASP cc_start: 0.8587 (t0) cc_final: 0.7938 (t0) REVERT: F 54 MET cc_start: 0.8648 (ptm) cc_final: 0.7670 (ptm) REVERT: F 90 GLN cc_start: 0.9276 (tm-30) cc_final: 0.9030 (tm-30) REVERT: F 150 GLN cc_start: 0.8977 (mm110) cc_final: 0.8707 (mm110) REVERT: F 391 ASP cc_start: 0.8929 (t70) cc_final: 0.8606 (m-30) REVERT: F 455 MET cc_start: 0.8454 (tmm) cc_final: 0.8160 (tmm) REVERT: F 521 LEU cc_start: 0.9284 (mm) cc_final: 0.8929 (tt) REVERT: G 49 TYR cc_start: 0.8096 (t80) cc_final: 0.7701 (t80) REVERT: G 54 MET cc_start: 0.8606 (ptm) cc_final: 0.7657 (ptm) REVERT: G 58 LEU cc_start: 0.8876 (mm) cc_final: 0.8643 (mm) REVERT: G 90 GLN cc_start: 0.9310 (tm-30) cc_final: 0.8983 (tm-30) REVERT: G 391 ASP cc_start: 0.8872 (t0) cc_final: 0.8648 (m-30) REVERT: G 455 MET cc_start: 0.8591 (tmm) cc_final: 0.8277 (tmm) REVERT: G 521 LEU cc_start: 0.9199 (tp) cc_final: 0.8785 (tt) REVERT: G 526 ASP cc_start: 0.8538 (t0) cc_final: 0.7287 (t0) REVERT: H 49 TYR cc_start: 0.8167 (t80) cc_final: 0.7834 (t80) REVERT: H 90 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8946 (tm-30) REVERT: H 455 MET cc_start: 0.8483 (tmm) cc_final: 0.8164 (tmm) REVERT: H 494 GLU cc_start: 0.7587 (mp0) cc_final: 0.7069 (mp0) REVERT: H 526 ASP cc_start: 0.8617 (t0) cc_final: 0.7831 (t0) REVERT: I 54 MET cc_start: 0.9084 (pmm) cc_final: 0.8830 (ptp) REVERT: I 90 GLN cc_start: 0.9308 (tm-30) cc_final: 0.9018 (tm-30) REVERT: I 391 ASP cc_start: 0.8907 (t70) cc_final: 0.8597 (m-30) REVERT: I 455 MET cc_start: 0.8548 (tmm) cc_final: 0.8166 (tmm) REVERT: I 494 GLU cc_start: 0.7680 (mp0) cc_final: 0.7333 (mp0) REVERT: J 90 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8967 (tm-30) REVERT: K 49 TYR cc_start: 0.8189 (t80) cc_final: 0.7867 (t80) REVERT: K 90 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8991 (tm-30) REVERT: K 104 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8443 (mtmt) REVERT: K 150 GLN cc_start: 0.9213 (mm110) cc_final: 0.8842 (mm110) REVERT: K 455 MET cc_start: 0.8542 (tmm) cc_final: 0.8132 (tmm) REVERT: K 471 GLN cc_start: 0.9222 (tt0) cc_final: 0.8979 (tt0) REVERT: K 494 GLU cc_start: 0.7617 (mp0) cc_final: 0.7364 (mp0) REVERT: K 526 ASP cc_start: 0.8597 (t0) cc_final: 0.7980 (t0) REVERT: L 54 MET cc_start: 0.8655 (ptm) cc_final: 0.7694 (ptm) REVERT: L 90 GLN cc_start: 0.9276 (tm-30) cc_final: 0.9030 (tm-30) REVERT: L 150 GLN cc_start: 0.8973 (mm110) cc_final: 0.8705 (mm110) REVERT: L 391 ASP cc_start: 0.8929 (t70) cc_final: 0.8610 (m-30) REVERT: L 455 MET cc_start: 0.8449 (tmm) cc_final: 0.8154 (tmm) REVERT: L 521 LEU cc_start: 0.9284 (mm) cc_final: 0.8929 (tt) REVERT: M 49 TYR cc_start: 0.8084 (t80) cc_final: 0.7697 (t80) REVERT: M 54 MET cc_start: 0.8607 (ptm) cc_final: 0.7653 (ptm) REVERT: M 58 LEU cc_start: 0.8890 (mm) cc_final: 0.8666 (mm) REVERT: M 90 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8982 (tm-30) REVERT: M 391 ASP cc_start: 0.8852 (t0) cc_final: 0.8633 (m-30) REVERT: M 455 MET cc_start: 0.8597 (tmm) cc_final: 0.8292 (tmm) REVERT: M 521 LEU cc_start: 0.9202 (tp) cc_final: 0.8786 (tt) REVERT: M 526 ASP cc_start: 0.8533 (t0) cc_final: 0.7271 (t0) REVERT: N 49 TYR cc_start: 0.8172 (t80) cc_final: 0.7836 (t80) REVERT: N 90 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8953 (tm-30) REVERT: N 455 MET cc_start: 0.8472 (tmm) cc_final: 0.8162 (tmm) REVERT: N 471 GLN cc_start: 0.9251 (tt0) cc_final: 0.9029 (tt0) REVERT: N 494 GLU cc_start: 0.7586 (mp0) cc_final: 0.7074 (mp0) REVERT: N 526 ASP cc_start: 0.8616 (t0) cc_final: 0.7831 (t0) REVERT: O 57 MET cc_start: 0.8530 (ppp) cc_final: 0.8322 (ppp) REVERT: O 90 GLN cc_start: 0.9310 (tm-30) cc_final: 0.9025 (tm-30) REVERT: O 391 ASP cc_start: 0.8911 (t70) cc_final: 0.8595 (m-30) REVERT: O 455 MET cc_start: 0.8546 (tmm) cc_final: 0.8166 (tmm) REVERT: O 494 GLU cc_start: 0.7687 (mp0) cc_final: 0.7355 (mp0) REVERT: O 521 LEU cc_start: 0.9329 (mm) cc_final: 0.8997 (tt) REVERT: P 49 TYR cc_start: 0.8064 (t80) cc_final: 0.7730 (t80) REVERT: Q 54 MET cc_start: 0.8663 (ptm) cc_final: 0.7603 (ptm) REVERT: Q 55 ASP cc_start: 0.8600 (m-30) cc_final: 0.8253 (m-30) REVERT: Q 90 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8953 (tm-30) REVERT: Q 455 MET cc_start: 0.8417 (tmm) cc_final: 0.8209 (tmm) REVERT: Q 526 ASP cc_start: 0.8593 (t0) cc_final: 0.7928 (t0) REVERT: R 90 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8952 (tm-30) REVERT: R 104 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8375 (mtmt) REVERT: R 177 ARG cc_start: 0.8285 (mtt180) cc_final: 0.8061 (mtt90) REVERT: R 455 MET cc_start: 0.8412 (tmm) cc_final: 0.8117 (tmm) REVERT: R 526 ASP cc_start: 0.8687 (t0) cc_final: 0.7788 (t0) outliers start: 1 outliers final: 0 residues processed: 794 average time/residue: 0.5210 time to fit residues: 712.7589 Evaluate side-chains 594 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 681 optimal weight: 0.0670 chunk 464 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 608 optimal weight: 5.9990 chunk 337 optimal weight: 0.4980 chunk 697 optimal weight: 1.9990 chunk 565 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 417 optimal weight: 0.7980 chunk 733 optimal weight: 50.0000 chunk 206 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 95 GLN E 126 HIS ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS F 460 ASN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS H 95 GLN H 126 HIS ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS K 95 GLN K 126 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 HIS ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 HIS N 95 GLN N 126 HIS ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS O 460 ASN P 95 GLN P 126 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 HIS ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 58968 Z= 0.131 Angle : 0.546 7.433 80172 Z= 0.274 Chirality : 0.040 0.168 9954 Planarity : 0.003 0.090 10386 Dihedral : 5.662 63.645 9000 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.86 (0.09), residues: 8226 helix: 1.00 (0.08), residues: 4446 sheet: 1.32 (0.15), residues: 1188 loop : -0.42 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 483 HIS 0.002 0.000 HIS A 126 PHE 0.001 0.000 PHE P 489 TYR 0.012 0.001 TYR F 431 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 938 time to evaluate : 5.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7876 (t80) cc_final: 0.7607 (t80) REVERT: A 201 VAL cc_start: 0.8749 (t) cc_final: 0.7936 (t) REVERT: A 455 MET cc_start: 0.8376 (tmm) cc_final: 0.8141 (tmm) REVERT: A 487 ASN cc_start: 0.6715 (t0) cc_final: 0.6120 (t0) REVERT: B 54 MET cc_start: 0.8342 (ptp) cc_final: 0.7416 (ptm) REVERT: C 90 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8910 (tm-30) REVERT: C 455 MET cc_start: 0.8378 (tmm) cc_final: 0.8019 (tmm) REVERT: C 487 ASN cc_start: 0.7471 (t0) cc_final: 0.6254 (t0) REVERT: C 526 ASP cc_start: 0.8446 (t0) cc_final: 0.7467 (t70) REVERT: D 90 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8950 (tm-30) REVERT: D 455 MET cc_start: 0.8321 (tmm) cc_final: 0.8096 (tmm) REVERT: D 471 GLN cc_start: 0.9197 (tt0) cc_final: 0.8996 (tt0) REVERT: D 487 ASN cc_start: 0.7322 (t0) cc_final: 0.6998 (t0) REVERT: D 526 ASP cc_start: 0.8483 (t0) cc_final: 0.8210 (t70) REVERT: E 49 TYR cc_start: 0.8005 (t80) cc_final: 0.7619 (t80) REVERT: E 455 MET cc_start: 0.8523 (tmm) cc_final: 0.8094 (tmm) REVERT: E 471 GLN cc_start: 0.9209 (tt0) cc_final: 0.8954 (tt0) REVERT: E 487 ASN cc_start: 0.7307 (t0) cc_final: 0.6988 (t0) REVERT: E 494 GLU cc_start: 0.7608 (mp0) cc_final: 0.7214 (mp0) REVERT: E 526 ASP cc_start: 0.8281 (t0) cc_final: 0.7867 (t0) REVERT: F 54 MET cc_start: 0.8561 (ptm) cc_final: 0.7468 (ptm) REVERT: F 90 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8996 (tm-30) REVERT: F 391 ASP cc_start: 0.8893 (t70) cc_final: 0.8571 (m-30) REVERT: F 455 MET cc_start: 0.8381 (tmm) cc_final: 0.8052 (tmm) REVERT: F 487 ASN cc_start: 0.7441 (t0) cc_final: 0.6936 (t0) REVERT: G 49 TYR cc_start: 0.7850 (t80) cc_final: 0.7573 (t80) REVERT: G 54 MET cc_start: 0.8541 (ptm) cc_final: 0.7541 (ptm) REVERT: G 58 LEU cc_start: 0.8797 (mm) cc_final: 0.8316 (mm) REVERT: G 90 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8922 (tm-30) REVERT: G 391 ASP cc_start: 0.8848 (t0) cc_final: 0.8635 (m-30) REVERT: G 455 MET cc_start: 0.8540 (tmm) cc_final: 0.8196 (tmm) REVERT: G 471 GLN cc_start: 0.9252 (tt0) cc_final: 0.9032 (tt0) REVERT: G 487 ASN cc_start: 0.6489 (t0) cc_final: 0.6123 (t0) REVERT: G 521 LEU cc_start: 0.9218 (tp) cc_final: 0.8861 (tt) REVERT: G 526 ASP cc_start: 0.8432 (t0) cc_final: 0.6889 (t0) REVERT: G 528 ILE cc_start: 0.9293 (mm) cc_final: 0.8910 (pt) REVERT: H 49 TYR cc_start: 0.8004 (t80) cc_final: 0.7647 (t80) REVERT: H 90 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8949 (tm-30) REVERT: H 455 MET cc_start: 0.8432 (tmm) cc_final: 0.8098 (tmm) REVERT: H 487 ASN cc_start: 0.7527 (t0) cc_final: 0.6205 (t0) REVERT: H 494 GLU cc_start: 0.7632 (mp0) cc_final: 0.7338 (mp0) REVERT: H 526 ASP cc_start: 0.8632 (t0) cc_final: 0.7581 (t0) REVERT: I 112 GLU cc_start: 0.7972 (tp30) cc_final: 0.7765 (tp30) REVERT: I 391 ASP cc_start: 0.8904 (t70) cc_final: 0.8583 (m-30) REVERT: I 455 MET cc_start: 0.8475 (tmm) cc_final: 0.8062 (tmm) REVERT: I 487 ASN cc_start: 0.7492 (t0) cc_final: 0.6026 (t0) REVERT: I 494 GLU cc_start: 0.7510 (mp0) cc_final: 0.7205 (mp0) REVERT: I 526 ASP cc_start: 0.8337 (t0) cc_final: 0.7630 (t70) REVERT: J 57 MET cc_start: 0.8396 (ppp) cc_final: 0.8184 (ppp) REVERT: J 90 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8943 (tm-30) REVERT: J 455 MET cc_start: 0.8308 (tmm) cc_final: 0.8090 (tmm) REVERT: J 471 GLN cc_start: 0.9201 (tt0) cc_final: 0.8966 (tt0) REVERT: J 487 ASN cc_start: 0.7327 (t0) cc_final: 0.7008 (t0) REVERT: K 49 TYR cc_start: 0.7953 (t80) cc_final: 0.7678 (t80) REVERT: K 104 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8492 (mtmt) REVERT: K 112 GLU cc_start: 0.7958 (tp30) cc_final: 0.7722 (tp30) REVERT: K 455 MET cc_start: 0.8509 (tmm) cc_final: 0.8099 (tmm) REVERT: K 471 GLN cc_start: 0.9210 (tt0) cc_final: 0.8956 (tt0) REVERT: K 487 ASN cc_start: 0.7310 (t0) cc_final: 0.7007 (t0) REVERT: K 494 GLU cc_start: 0.7608 (mp0) cc_final: 0.7215 (mp0) REVERT: K 526 ASP cc_start: 0.8327 (t0) cc_final: 0.7908 (t0) REVERT: L 54 MET cc_start: 0.8565 (ptm) cc_final: 0.7454 (ptm) REVERT: L 90 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8996 (tm-30) REVERT: L 112 GLU cc_start: 0.7990 (tp30) cc_final: 0.7779 (tp30) REVERT: L 391 ASP cc_start: 0.8888 (t70) cc_final: 0.8568 (m-30) REVERT: L 455 MET cc_start: 0.8371 (tmm) cc_final: 0.8051 (tmm) REVERT: L 487 ASN cc_start: 0.7438 (t0) cc_final: 0.7087 (t0) REVERT: M 49 TYR cc_start: 0.7842 (t80) cc_final: 0.7551 (t80) REVERT: M 54 MET cc_start: 0.8532 (ptm) cc_final: 0.7536 (ptm) REVERT: M 58 LEU cc_start: 0.8782 (mm) cc_final: 0.8291 (mm) REVERT: M 90 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8921 (tm-30) REVERT: M 391 ASP cc_start: 0.8839 (t0) cc_final: 0.8618 (m-30) REVERT: M 455 MET cc_start: 0.8536 (tmm) cc_final: 0.8195 (tmm) REVERT: M 471 GLN cc_start: 0.9251 (tt0) cc_final: 0.9030 (tt0) REVERT: M 487 ASN cc_start: 0.6480 (t0) cc_final: 0.6105 (t0) REVERT: M 521 LEU cc_start: 0.9216 (tp) cc_final: 0.8863 (tt) REVERT: M 526 ASP cc_start: 0.8427 (t0) cc_final: 0.7027 (t0) REVERT: M 528 ILE cc_start: 0.9290 (mm) cc_final: 0.8910 (pt) REVERT: N 49 TYR cc_start: 0.8001 (t80) cc_final: 0.7644 (t80) REVERT: N 90 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8946 (tm-30) REVERT: N 455 MET cc_start: 0.8434 (tmm) cc_final: 0.8100 (tmm) REVERT: N 487 ASN cc_start: 0.7521 (t0) cc_final: 0.6196 (t0) REVERT: N 494 GLU cc_start: 0.7623 (mp0) cc_final: 0.7338 (mp0) REVERT: N 526 ASP cc_start: 0.8633 (t0) cc_final: 0.7564 (t0) REVERT: O 90 GLN cc_start: 0.9271 (tm-30) cc_final: 0.9032 (tm-30) REVERT: O 391 ASP cc_start: 0.8902 (t70) cc_final: 0.8581 (m-30) REVERT: O 455 MET cc_start: 0.8490 (tmm) cc_final: 0.8079 (tmm) REVERT: O 487 ASN cc_start: 0.7502 (t0) cc_final: 0.6005 (t0) REVERT: O 494 GLU cc_start: 0.7533 (mp0) cc_final: 0.7241 (mp0) REVERT: P 49 TYR cc_start: 0.7872 (t80) cc_final: 0.7603 (t80) REVERT: P 201 VAL cc_start: 0.8746 (t) cc_final: 0.7934 (t) REVERT: P 455 MET cc_start: 0.8373 (tmm) cc_final: 0.8136 (tmm) REVERT: P 487 ASN cc_start: 0.6720 (t0) cc_final: 0.6123 (t0) REVERT: Q 54 MET cc_start: 0.8288 (ptp) cc_final: 0.7384 (ptm) REVERT: Q 455 MET cc_start: 0.8376 (tmm) cc_final: 0.8154 (tmm) REVERT: R 74 ILE cc_start: 0.9271 (mt) cc_final: 0.9038 (mt) REVERT: R 90 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8888 (tm-30) REVERT: R 455 MET cc_start: 0.8365 (tmm) cc_final: 0.8016 (tmm) REVERT: R 487 ASN cc_start: 0.7457 (t0) cc_final: 0.6231 (t0) REVERT: R 526 ASP cc_start: 0.8438 (t0) cc_final: 0.7466 (t70) outliers start: 3 outliers final: 2 residues processed: 938 average time/residue: 0.5091 time to fit residues: 826.6591 Evaluate side-chains 706 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 704 time to evaluate : 4.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 275 optimal weight: 0.7980 chunk 736 optimal weight: 10.0000 chunk 161 optimal weight: 30.0000 chunk 480 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 818 optimal weight: 40.0000 chunk 679 optimal weight: 0.2980 chunk 378 optimal weight: 4.9990 chunk 68 optimal weight: 40.0000 chunk 270 optimal weight: 6.9990 chunk 429 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 126 HIS ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS K 95 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 HIS ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN N 126 HIS ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 58968 Z= 0.133 Angle : 0.535 9.740 80172 Z= 0.269 Chirality : 0.040 0.184 9954 Planarity : 0.003 0.046 10386 Dihedral : 5.321 56.740 9000 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.02 % Allowed : 0.92 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.94 (0.09), residues: 8226 helix: 1.01 (0.08), residues: 4482 sheet: 1.54 (0.15), residues: 1188 loop : -0.38 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 199 HIS 0.002 0.000 HIS B 126 PHE 0.002 0.000 PHE Q 489 TYR 0.013 0.001 TYR B 484 ARG 0.005 0.000 ARG P 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 907 time to evaluate : 5.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7912 (t80) cc_final: 0.7703 (t80) REVERT: A 455 MET cc_start: 0.8381 (tmm) cc_final: 0.8114 (tmm) REVERT: A 470 MET cc_start: 0.8602 (tpp) cc_final: 0.8289 (tpp) REVERT: A 487 ASN cc_start: 0.7340 (t0) cc_final: 0.6812 (t0) REVERT: B 54 MET cc_start: 0.8185 (ptp) cc_final: 0.7393 (ptm) REVERT: B 57 MET cc_start: 0.8428 (ppp) cc_final: 0.8178 (ppp) REVERT: B 177 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7335 (mtt90) REVERT: B 395 ARG cc_start: 0.9203 (mtm110) cc_final: 0.8905 (mtm110) REVERT: B 455 MET cc_start: 0.8360 (tmm) cc_final: 0.8138 (tmm) REVERT: B 526 ASP cc_start: 0.8116 (t0) cc_final: 0.7697 (t70) REVERT: C 90 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8902 (tm-30) REVERT: C 455 MET cc_start: 0.8357 (tmm) cc_final: 0.8011 (tmm) REVERT: C 487 ASN cc_start: 0.6504 (t0) cc_final: 0.6070 (t0) REVERT: C 526 ASP cc_start: 0.8495 (t0) cc_final: 0.7613 (t70) REVERT: D 90 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8951 (tm-30) REVERT: D 471 GLN cc_start: 0.9194 (tt0) cc_final: 0.8936 (tt0) REVERT: D 487 ASN cc_start: 0.7374 (t0) cc_final: 0.7081 (t0) REVERT: D 526 ASP cc_start: 0.8531 (t0) cc_final: 0.8294 (t70) REVERT: E 49 TYR cc_start: 0.7928 (t80) cc_final: 0.7607 (t80) REVERT: E 455 MET cc_start: 0.8507 (tmm) cc_final: 0.8078 (tmm) REVERT: E 471 GLN cc_start: 0.9206 (tt0) cc_final: 0.8964 (tt0) REVERT: E 494 GLU cc_start: 0.7631 (mp0) cc_final: 0.7219 (mp0) REVERT: E 526 ASP cc_start: 0.8311 (t0) cc_final: 0.7926 (t0) REVERT: F 54 MET cc_start: 0.8249 (ptm) cc_final: 0.7144 (ptm) REVERT: F 90 GLN cc_start: 0.9263 (tm-30) cc_final: 0.9007 (tm-30) REVERT: F 115 LYS cc_start: 0.9293 (ttpt) cc_final: 0.9061 (tmtt) REVERT: F 391 ASP cc_start: 0.8885 (t70) cc_final: 0.8558 (m-30) REVERT: F 423 GLU cc_start: 0.8525 (tt0) cc_final: 0.8306 (mm-30) REVERT: F 455 MET cc_start: 0.8424 (tmm) cc_final: 0.8040 (tmm) REVERT: F 487 ASN cc_start: 0.7349 (t0) cc_final: 0.6887 (t0) REVERT: G 49 TYR cc_start: 0.7948 (t80) cc_final: 0.7639 (t80) REVERT: G 54 MET cc_start: 0.8443 (ptm) cc_final: 0.7402 (ptm) REVERT: G 58 LEU cc_start: 0.8800 (mm) cc_final: 0.8511 (mm) REVERT: G 90 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8973 (tm-30) REVERT: G 391 ASP cc_start: 0.8808 (t0) cc_final: 0.8592 (m-30) REVERT: G 455 MET cc_start: 0.8519 (tmm) cc_final: 0.8205 (tmm) REVERT: G 521 LEU cc_start: 0.9171 (tp) cc_final: 0.8874 (tt) REVERT: G 526 ASP cc_start: 0.8400 (t0) cc_final: 0.7137 (t0) REVERT: G 528 ILE cc_start: 0.9334 (mm) cc_final: 0.8988 (pt) REVERT: H 49 TYR cc_start: 0.7962 (t80) cc_final: 0.7411 (t80) REVERT: H 55 ASP cc_start: 0.8324 (m-30) cc_final: 0.8001 (m-30) REVERT: H 90 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8921 (tm-30) REVERT: H 455 MET cc_start: 0.8487 (tmm) cc_final: 0.8087 (tmm) REVERT: H 487 ASN cc_start: 0.7517 (t0) cc_final: 0.6461 (t0) REVERT: H 521 LEU cc_start: 0.9259 (tp) cc_final: 0.8954 (tt) REVERT: H 526 ASP cc_start: 0.8540 (t0) cc_final: 0.7290 (t0) REVERT: I 55 ASP cc_start: 0.8368 (m-30) cc_final: 0.7834 (m-30) REVERT: I 391 ASP cc_start: 0.8882 (t70) cc_final: 0.8583 (m-30) REVERT: I 455 MET cc_start: 0.8463 (tmm) cc_final: 0.8084 (tmm) REVERT: I 487 ASN cc_start: 0.7612 (t0) cc_final: 0.5913 (t0) REVERT: I 526 ASP cc_start: 0.8180 (t0) cc_final: 0.7577 (t0) REVERT: J 90 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8948 (tm-30) REVERT: J 399 ASP cc_start: 0.9178 (m-30) cc_final: 0.8976 (m-30) REVERT: J 471 GLN cc_start: 0.9193 (tt0) cc_final: 0.8943 (tt0) REVERT: J 487 ASN cc_start: 0.7364 (t0) cc_final: 0.6908 (t0) REVERT: K 49 TYR cc_start: 0.7813 (t80) cc_final: 0.7559 (t80) REVERT: K 455 MET cc_start: 0.8502 (tmm) cc_final: 0.8065 (tmm) REVERT: K 471 GLN cc_start: 0.9209 (tt0) cc_final: 0.8987 (tt0) REVERT: K 494 GLU cc_start: 0.7627 (mp0) cc_final: 0.7245 (mp0) REVERT: K 526 ASP cc_start: 0.8320 (t0) cc_final: 0.7959 (t0) REVERT: L 54 MET cc_start: 0.8244 (ptm) cc_final: 0.7151 (ptm) REVERT: L 90 GLN cc_start: 0.9262 (tm-30) cc_final: 0.9006 (tm-30) REVERT: L 115 LYS cc_start: 0.9293 (ttpt) cc_final: 0.9059 (tmtt) REVERT: L 391 ASP cc_start: 0.8882 (t70) cc_final: 0.8556 (m-30) REVERT: L 423 GLU cc_start: 0.8522 (tt0) cc_final: 0.8308 (mm-30) REVERT: L 455 MET cc_start: 0.8427 (tmm) cc_final: 0.8035 (tmm) REVERT: L 487 ASN cc_start: 0.7351 (t0) cc_final: 0.6883 (t0) REVERT: M 49 TYR cc_start: 0.7954 (t80) cc_final: 0.7637 (t80) REVERT: M 54 MET cc_start: 0.8441 (ptm) cc_final: 0.7459 (ptm) REVERT: M 58 LEU cc_start: 0.8798 (mm) cc_final: 0.8193 (mm) REVERT: M 90 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8972 (tm-30) REVERT: M 391 ASP cc_start: 0.8805 (t0) cc_final: 0.8589 (m-30) REVERT: M 455 MET cc_start: 0.8518 (tmm) cc_final: 0.8198 (tmm) REVERT: M 521 LEU cc_start: 0.9169 (tp) cc_final: 0.8869 (tt) REVERT: M 526 ASP cc_start: 0.8392 (t0) cc_final: 0.7137 (t0) REVERT: M 528 ILE cc_start: 0.9324 (mm) cc_final: 0.8971 (pt) REVERT: N 49 TYR cc_start: 0.7963 (t80) cc_final: 0.7403 (t80) REVERT: N 55 ASP cc_start: 0.8311 (m-30) cc_final: 0.8064 (m-30) REVERT: N 90 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8932 (tm-30) REVERT: N 455 MET cc_start: 0.8483 (tmm) cc_final: 0.8088 (tmm) REVERT: N 487 ASN cc_start: 0.7513 (t0) cc_final: 0.6454 (t0) REVERT: N 521 LEU cc_start: 0.9255 (tp) cc_final: 0.8949 (tt) REVERT: N 526 ASP cc_start: 0.8547 (t0) cc_final: 0.7314 (t0) REVERT: O 90 GLN cc_start: 0.9259 (tm-30) cc_final: 0.9039 (tm-30) REVERT: O 391 ASP cc_start: 0.8874 (t70) cc_final: 0.8575 (m-30) REVERT: O 455 MET cc_start: 0.8462 (tmm) cc_final: 0.8064 (tmm) REVERT: O 487 ASN cc_start: 0.7568 (t0) cc_final: 0.5877 (t0) REVERT: P 49 TYR cc_start: 0.7914 (t80) cc_final: 0.7704 (t80) REVERT: P 455 MET cc_start: 0.8372 (tmm) cc_final: 0.8111 (tmm) REVERT: P 470 MET cc_start: 0.8603 (tpp) cc_final: 0.8285 (tpp) REVERT: P 487 ASN cc_start: 0.7345 (t0) cc_final: 0.6807 (t0) REVERT: Q 54 MET cc_start: 0.8187 (ptp) cc_final: 0.7384 (ptm) REVERT: Q 57 MET cc_start: 0.8394 (ppp) cc_final: 0.8141 (ppp) REVERT: Q 177 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7346 (mtt90) REVERT: Q 395 ARG cc_start: 0.9200 (mtm110) cc_final: 0.8900 (mtm110) REVERT: Q 526 ASP cc_start: 0.8114 (t0) cc_final: 0.7688 (t70) REVERT: R 58 LEU cc_start: 0.8237 (mm) cc_final: 0.7588 (mm) REVERT: R 90 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8891 (tm-30) REVERT: R 455 MET cc_start: 0.8349 (tmm) cc_final: 0.8002 (tmm) REVERT: R 487 ASN cc_start: 0.6530 (t0) cc_final: 0.6089 (t0) REVERT: R 526 ASP cc_start: 0.8487 (t0) cc_final: 0.7624 (t70) outliers start: 1 outliers final: 0 residues processed: 907 average time/residue: 0.5116 time to fit residues: 805.1904 Evaluate side-chains 689 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 689 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 789 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 466 optimal weight: 0.0770 chunk 597 optimal weight: 0.8980 chunk 463 optimal weight: 1.9990 chunk 689 optimal weight: 10.0000 chunk 457 optimal weight: 0.9980 chunk 815 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 497 optimal weight: 50.0000 chunk 376 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN ** M 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** N 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN ** R 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 58968 Z= 0.127 Angle : 0.530 7.608 80172 Z= 0.262 Chirality : 0.040 0.188 9954 Planarity : 0.003 0.054 10386 Dihedral : 5.158 57.170 9000 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.10 % Allowed : 1.00 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.10 (0.09), residues: 8226 helix: 1.16 (0.08), residues: 4536 sheet: 1.63 (0.15), residues: 1188 loop : -0.41 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 483 HIS 0.002 0.001 HIS J 126 PHE 0.011 0.001 PHE P 489 TYR 0.013 0.001 TYR I 484 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 875 time to evaluate : 5.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8374 (tmm) cc_final: 0.8166 (tmm) REVERT: B 55 ASP cc_start: 0.8083 (m-30) cc_final: 0.7730 (m-30) REVERT: B 455 MET cc_start: 0.8350 (tmm) cc_final: 0.8140 (tmm) REVERT: B 526 ASP cc_start: 0.8134 (t0) cc_final: 0.7631 (t0) REVERT: C 90 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8904 (tm-30) REVERT: C 95 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7532 (tp-100) REVERT: C 177 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7182 (mtt90) REVERT: C 455 MET cc_start: 0.8383 (tmm) cc_final: 0.8015 (tmm) REVERT: C 487 ASN cc_start: 0.6588 (t0) cc_final: 0.6232 (t0) REVERT: D 55 ASP cc_start: 0.8290 (m-30) cc_final: 0.7823 (m-30) REVERT: D 90 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8943 (tm-30) REVERT: D 455 MET cc_start: 0.8344 (tmm) cc_final: 0.8050 (tmm) REVERT: D 471 GLN cc_start: 0.9207 (tt0) cc_final: 0.8946 (tt0) REVERT: D 487 ASN cc_start: 0.7391 (t0) cc_final: 0.7085 (t0) REVERT: D 526 ASP cc_start: 0.8514 (t0) cc_final: 0.8308 (t70) REVERT: E 49 TYR cc_start: 0.7890 (t80) cc_final: 0.7630 (t80) REVERT: E 54 MET cc_start: 0.8203 (ppp) cc_final: 0.7957 (ppp) REVERT: E 455 MET cc_start: 0.8482 (tmm) cc_final: 0.8064 (tmm) REVERT: E 471 GLN cc_start: 0.9206 (tt0) cc_final: 0.8966 (tt0) REVERT: E 494 GLU cc_start: 0.7652 (mp0) cc_final: 0.7067 (mp0) REVERT: E 526 ASP cc_start: 0.8205 (t0) cc_final: 0.7739 (t0) REVERT: F 54 MET cc_start: 0.8317 (ptm) cc_final: 0.7127 (ptm) REVERT: F 90 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9010 (tm-30) REVERT: F 115 LYS cc_start: 0.9276 (ttpt) cc_final: 0.8977 (tmtt) REVERT: F 391 ASP cc_start: 0.8845 (t70) cc_final: 0.8530 (m-30) REVERT: F 455 MET cc_start: 0.8428 (tmm) cc_final: 0.8079 (tmm) REVERT: F 487 ASN cc_start: 0.7344 (t0) cc_final: 0.7006 (t0) REVERT: G 49 TYR cc_start: 0.8032 (t80) cc_final: 0.7712 (t80) REVERT: G 54 MET cc_start: 0.8374 (ptm) cc_final: 0.7309 (ptm) REVERT: G 108 ILE cc_start: 0.9190 (tp) cc_final: 0.8825 (tp) REVERT: G 112 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7809 (mm-30) REVERT: G 177 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6590 (mpp80) REVERT: G 391 ASP cc_start: 0.8785 (t0) cc_final: 0.8567 (m-30) REVERT: G 455 MET cc_start: 0.8519 (tmm) cc_final: 0.8176 (tmm) REVERT: G 471 GLN cc_start: 0.9221 (tt0) cc_final: 0.8989 (tt0) REVERT: G 521 LEU cc_start: 0.9176 (tp) cc_final: 0.8903 (tt) REVERT: G 526 ASP cc_start: 0.8295 (t0) cc_final: 0.7007 (t0) REVERT: G 528 ILE cc_start: 0.9351 (mm) cc_final: 0.8967 (pt) REVERT: H 49 TYR cc_start: 0.7936 (t80) cc_final: 0.7449 (t80) REVERT: H 90 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8940 (tm-30) REVERT: H 455 MET cc_start: 0.8465 (tmm) cc_final: 0.8095 (tmm) REVERT: H 487 ASN cc_start: 0.7482 (t0) cc_final: 0.6822 (t0) REVERT: H 494 GLU cc_start: 0.7678 (mp0) cc_final: 0.7397 (mp0) REVERT: H 521 LEU cc_start: 0.9264 (tp) cc_final: 0.9057 (tt) REVERT: H 526 ASP cc_start: 0.8530 (t0) cc_final: 0.7346 (t0) REVERT: I 42 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7868 (tm-30) REVERT: I 55 ASP cc_start: 0.8391 (m-30) cc_final: 0.7804 (m-30) REVERT: I 108 ILE cc_start: 0.9261 (tp) cc_final: 0.8737 (tp) REVERT: I 112 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7704 (mm-30) REVERT: I 391 ASP cc_start: 0.8863 (t70) cc_final: 0.8570 (m-30) REVERT: I 455 MET cc_start: 0.8465 (tmm) cc_final: 0.8072 (tmm) REVERT: I 487 ASN cc_start: 0.6644 (t0) cc_final: 0.6117 (t0) REVERT: I 526 ASP cc_start: 0.8264 (t0) cc_final: 0.7842 (t0) REVERT: J 55 ASP cc_start: 0.8259 (m-30) cc_final: 0.7797 (m-30) REVERT: J 399 ASP cc_start: 0.9172 (m-30) cc_final: 0.8962 (m-30) REVERT: J 455 MET cc_start: 0.8322 (tmm) cc_final: 0.8035 (tmm) REVERT: J 471 GLN cc_start: 0.9200 (tt0) cc_final: 0.8946 (tt0) REVERT: J 487 ASN cc_start: 0.7398 (t0) cc_final: 0.7085 (t0) REVERT: K 49 TYR cc_start: 0.7999 (t80) cc_final: 0.7564 (t80) REVERT: K 54 MET cc_start: 0.8176 (ppp) cc_final: 0.7952 (ppp) REVERT: K 455 MET cc_start: 0.8472 (tmm) cc_final: 0.8047 (tmm) REVERT: K 471 GLN cc_start: 0.9210 (tt0) cc_final: 0.8973 (tt0) REVERT: K 494 GLU cc_start: 0.7610 (mp0) cc_final: 0.7118 (mp0) REVERT: K 526 ASP cc_start: 0.8221 (t0) cc_final: 0.7970 (t0) REVERT: L 54 MET cc_start: 0.8282 (ptm) cc_final: 0.8025 (ptm) REVERT: L 90 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8980 (tm-30) REVERT: L 115 LYS cc_start: 0.9273 (ttpt) cc_final: 0.8980 (tmtt) REVERT: L 391 ASP cc_start: 0.8842 (t70) cc_final: 0.8528 (m-30) REVERT: L 455 MET cc_start: 0.8421 (tmm) cc_final: 0.8072 (tmm) REVERT: L 487 ASN cc_start: 0.7345 (t0) cc_final: 0.7003 (t0) REVERT: M 49 TYR cc_start: 0.8027 (t80) cc_final: 0.7703 (t80) REVERT: M 54 MET cc_start: 0.8290 (ptm) cc_final: 0.7046 (ptm) REVERT: M 55 ASP cc_start: 0.8405 (m-30) cc_final: 0.7858 (m-30) REVERT: M 108 ILE cc_start: 0.9192 (tp) cc_final: 0.8825 (tp) REVERT: M 112 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7809 (mm-30) REVERT: M 177 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6593 (mpp80) REVERT: M 391 ASP cc_start: 0.8776 (t0) cc_final: 0.8568 (m-30) REVERT: M 455 MET cc_start: 0.8530 (tmm) cc_final: 0.8181 (tmm) REVERT: M 471 GLN cc_start: 0.9254 (tt0) cc_final: 0.9001 (tt0) REVERT: M 521 LEU cc_start: 0.9170 (tp) cc_final: 0.8897 (tt) REVERT: M 528 ILE cc_start: 0.9315 (mm) cc_final: 0.8910 (pt) REVERT: N 49 TYR cc_start: 0.7938 (t80) cc_final: 0.7446 (t80) REVERT: N 90 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8926 (tm-30) REVERT: N 455 MET cc_start: 0.8465 (tmm) cc_final: 0.8095 (tmm) REVERT: N 487 ASN cc_start: 0.7477 (t0) cc_final: 0.6829 (t0) REVERT: N 494 GLU cc_start: 0.7667 (mp0) cc_final: 0.7386 (mp0) REVERT: N 521 LEU cc_start: 0.9268 (tp) cc_final: 0.9054 (tt) REVERT: N 526 ASP cc_start: 0.8493 (t0) cc_final: 0.7292 (t0) REVERT: O 42 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7904 (tm-30) REVERT: O 90 GLN cc_start: 0.9273 (tm-30) cc_final: 0.9014 (tm-30) REVERT: O 108 ILE cc_start: 0.9259 (tp) cc_final: 0.8521 (tp) REVERT: O 112 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7638 (mm-30) REVERT: O 391 ASP cc_start: 0.8867 (t70) cc_final: 0.8566 (m-30) REVERT: O 455 MET cc_start: 0.8450 (tmm) cc_final: 0.8058 (tmm) REVERT: O 487 ASN cc_start: 0.6673 (t0) cc_final: 0.6001 (t0) REVERT: O 526 ASP cc_start: 0.8430 (t0) cc_final: 0.8176 (t70) REVERT: P 455 MET cc_start: 0.8367 (tmm) cc_final: 0.8153 (tmm) REVERT: P 471 GLN cc_start: 0.9174 (tt0) cc_final: 0.8973 (tt0) REVERT: Q 55 ASP cc_start: 0.8083 (m-30) cc_final: 0.7742 (m-30) REVERT: Q 395 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8986 (mtm-85) REVERT: Q 455 MET cc_start: 0.8353 (tmm) cc_final: 0.8148 (tmm) REVERT: Q 526 ASP cc_start: 0.8138 (t0) cc_final: 0.7625 (t0) REVERT: R 90 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8892 (tm-30) REVERT: R 95 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7542 (tp-100) REVERT: R 177 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7191 (mtt90) REVERT: R 455 MET cc_start: 0.8373 (tmm) cc_final: 0.8015 (tmm) REVERT: R 487 ASN cc_start: 0.6592 (t0) cc_final: 0.6214 (t0) outliers start: 5 outliers final: 0 residues processed: 877 average time/residue: 0.4910 time to fit residues: 756.6639 Evaluate side-chains 677 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 675 time to evaluate : 5.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 504 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 487 optimal weight: 9.9990 chunk 245 optimal weight: 0.0770 chunk 160 optimal weight: 30.0000 chunk 157 optimal weight: 1.9990 chunk 518 optimal weight: 0.8980 chunk 555 optimal weight: 2.9990 chunk 403 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 640 optimal weight: 50.0000 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS G 95 GLN G 126 HIS H 95 GLN H 126 HIS ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS K 95 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 HIS M 95 GLN M 126 HIS N 95 GLN N 126 HIS ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58968 Z= 0.193 Angle : 0.568 8.074 80172 Z= 0.284 Chirality : 0.041 0.179 9954 Planarity : 0.003 0.056 10386 Dihedral : 5.245 58.386 9000 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.04 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.14 (0.09), residues: 8226 helix: 1.16 (0.08), residues: 4482 sheet: 1.77 (0.16), residues: 1098 loop : -0.27 (0.13), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 483 HIS 0.004 0.001 HIS J 126 PHE 0.012 0.001 PHE O 489 TYR 0.011 0.001 TYR Q 484 ARG 0.006 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 817 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8660 (ppp) cc_final: 0.8241 (ppp) REVERT: B 455 MET cc_start: 0.8406 (tmm) cc_final: 0.8191 (tmm) REVERT: B 526 ASP cc_start: 0.8176 (t0) cc_final: 0.7700 (t70) REVERT: C 90 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8941 (tm-30) REVERT: C 112 GLU cc_start: 0.8193 (tp30) cc_final: 0.7946 (tp30) REVERT: C 455 MET cc_start: 0.8440 (tmm) cc_final: 0.8059 (tmm) REVERT: C 487 ASN cc_start: 0.7202 (t0) cc_final: 0.6935 (t0) REVERT: C 526 ASP cc_start: 0.8625 (t0) cc_final: 0.8245 (t70) REVERT: D 90 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8941 (tm-30) REVERT: D 455 MET cc_start: 0.8396 (tmm) cc_final: 0.8150 (tmm) REVERT: D 487 ASN cc_start: 0.7531 (t0) cc_final: 0.7014 (t0) REVERT: E 49 TYR cc_start: 0.7945 (t80) cc_final: 0.7703 (t80) REVERT: E 54 MET cc_start: 0.8395 (ppp) cc_final: 0.7570 (ppp) REVERT: E 90 GLN cc_start: 0.9282 (tm-30) cc_final: 0.9049 (tm-30) REVERT: E 455 MET cc_start: 0.8512 (tmm) cc_final: 0.8162 (tmm) REVERT: E 471 GLN cc_start: 0.9209 (tt0) cc_final: 0.8949 (tt0) REVERT: E 494 GLU cc_start: 0.7607 (mp0) cc_final: 0.7073 (mp0) REVERT: E 526 ASP cc_start: 0.8438 (t0) cc_final: 0.7438 (t0) REVERT: F 54 MET cc_start: 0.8439 (ptp) cc_final: 0.7503 (ptm) REVERT: F 90 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9012 (tm-30) REVERT: F 391 ASP cc_start: 0.8865 (t70) cc_final: 0.8550 (m-30) REVERT: F 455 MET cc_start: 0.8510 (tmm) cc_final: 0.8193 (tmm) REVERT: F 487 ASN cc_start: 0.7438 (t0) cc_final: 0.6929 (t0) REVERT: G 49 TYR cc_start: 0.8118 (t80) cc_final: 0.7731 (t80) REVERT: G 55 ASP cc_start: 0.8313 (m-30) cc_final: 0.7868 (m-30) REVERT: G 391 ASP cc_start: 0.8818 (t0) cc_final: 0.8612 (m-30) REVERT: G 455 MET cc_start: 0.8536 (tmm) cc_final: 0.8228 (tmm) REVERT: G 471 GLN cc_start: 0.9232 (tt0) cc_final: 0.8991 (tt0) REVERT: G 521 LEU cc_start: 0.9181 (tp) cc_final: 0.8912 (tt) REVERT: G 526 ASP cc_start: 0.8248 (t0) cc_final: 0.7408 (t0) REVERT: H 49 TYR cc_start: 0.8073 (t80) cc_final: 0.7569 (t80) REVERT: H 90 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8955 (tm-30) REVERT: H 455 MET cc_start: 0.8529 (tmm) cc_final: 0.8153 (tmm) REVERT: H 487 ASN cc_start: 0.7588 (t0) cc_final: 0.7036 (t0) REVERT: H 494 GLU cc_start: 0.7732 (mp0) cc_final: 0.7293 (mp0) REVERT: H 521 LEU cc_start: 0.9301 (tp) cc_final: 0.9011 (tt) REVERT: I 55 ASP cc_start: 0.8401 (m-30) cc_final: 0.7741 (m-30) REVERT: I 455 MET cc_start: 0.8505 (tmm) cc_final: 0.8166 (tmm) REVERT: I 487 ASN cc_start: 0.6998 (t0) cc_final: 0.6292 (t0) REVERT: I 494 GLU cc_start: 0.8000 (pm20) cc_final: 0.7417 (pm20) REVERT: I 526 ASP cc_start: 0.8250 (t0) cc_final: 0.7603 (t0) REVERT: J 399 ASP cc_start: 0.9202 (m-30) cc_final: 0.8997 (m-30) REVERT: J 455 MET cc_start: 0.8376 (tmm) cc_final: 0.8149 (tmm) REVERT: J 487 ASN cc_start: 0.7485 (t0) cc_final: 0.6967 (t0) REVERT: K 49 TYR cc_start: 0.8051 (t80) cc_final: 0.7663 (t80) REVERT: K 54 MET cc_start: 0.8383 (ppp) cc_final: 0.7539 (ppp) REVERT: K 90 GLN cc_start: 0.9279 (tm-30) cc_final: 0.9043 (tm-30) REVERT: K 455 MET cc_start: 0.8526 (tmm) cc_final: 0.8175 (tmm) REVERT: K 471 GLN cc_start: 0.9213 (tt0) cc_final: 0.8955 (tt0) REVERT: K 494 GLU cc_start: 0.7600 (mp0) cc_final: 0.7087 (mp0) REVERT: L 54 MET cc_start: 0.8366 (ptp) cc_final: 0.7403 (ptm) REVERT: L 90 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9023 (tm-30) REVERT: L 391 ASP cc_start: 0.8863 (t70) cc_final: 0.8548 (m-30) REVERT: L 455 MET cc_start: 0.8491 (tmm) cc_final: 0.8176 (tmm) REVERT: L 487 ASN cc_start: 0.7460 (t0) cc_final: 0.6973 (t0) REVERT: M 49 TYR cc_start: 0.8124 (t80) cc_final: 0.7729 (t80) REVERT: M 55 ASP cc_start: 0.8508 (m-30) cc_final: 0.8066 (m-30) REVERT: M 391 ASP cc_start: 0.8815 (t0) cc_final: 0.8612 (m-30) REVERT: M 455 MET cc_start: 0.8543 (tmm) cc_final: 0.8243 (tmm) REVERT: M 521 LEU cc_start: 0.9179 (tp) cc_final: 0.8905 (tt) REVERT: M 526 ASP cc_start: 0.8344 (t0) cc_final: 0.7492 (t70) REVERT: N 49 TYR cc_start: 0.8080 (t80) cc_final: 0.7572 (t80) REVERT: N 90 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8959 (tm-30) REVERT: N 455 MET cc_start: 0.8514 (tmm) cc_final: 0.8149 (tmm) REVERT: N 487 ASN cc_start: 0.7599 (t0) cc_final: 0.7037 (t0) REVERT: N 494 GLU cc_start: 0.7719 (mp0) cc_final: 0.7288 (mp0) REVERT: N 521 LEU cc_start: 0.9303 (tp) cc_final: 0.9010 (tt) REVERT: O 54 MET cc_start: 0.8130 (ppp) cc_final: 0.7751 (ppp) REVERT: O 90 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9043 (tm-30) REVERT: O 455 MET cc_start: 0.8490 (tmm) cc_final: 0.8157 (tmm) REVERT: O 487 ASN cc_start: 0.7078 (t0) cc_final: 0.6678 (t0) REVERT: O 521 LEU cc_start: 0.9408 (tp) cc_final: 0.9191 (tt) REVERT: O 526 ASP cc_start: 0.8383 (t0) cc_final: 0.7924 (t70) REVERT: P 57 MET cc_start: 0.8650 (ppp) cc_final: 0.8240 (ppp) REVERT: Q 455 MET cc_start: 0.8401 (tmm) cc_final: 0.8170 (tmm) REVERT: Q 526 ASP cc_start: 0.8174 (t0) cc_final: 0.7697 (t70) REVERT: R 90 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8931 (tm-30) REVERT: R 112 GLU cc_start: 0.8179 (tp30) cc_final: 0.7943 (tp30) REVERT: R 455 MET cc_start: 0.8439 (tmm) cc_final: 0.8065 (tmm) REVERT: R 487 ASN cc_start: 0.7214 (t0) cc_final: 0.6957 (t0) REVERT: R 526 ASP cc_start: 0.8622 (t0) cc_final: 0.8213 (t70) outliers start: 2 outliers final: 2 residues processed: 819 average time/residue: 0.4953 time to fit residues: 714.2869 Evaluate side-chains 607 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 605 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 741 optimal weight: 0.9990 chunk 781 optimal weight: 8.9990 chunk 712 optimal weight: 4.9990 chunk 759 optimal weight: 9.9990 chunk 780 optimal weight: 30.0000 chunk 457 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 596 optimal weight: 50.0000 chunk 233 optimal weight: 0.6980 chunk 686 optimal weight: 40.0000 chunk 718 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS G 126 HIS H 95 GLN H 126 HIS ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN K 126 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 HIS M 126 HIS N 95 GLN N 126 HIS ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 58968 Z= 0.230 Angle : 0.601 6.754 80172 Z= 0.304 Chirality : 0.042 0.183 9954 Planarity : 0.004 0.059 10386 Dihedral : 5.387 58.851 9000 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.09 (0.09), residues: 8226 helix: 1.20 (0.08), residues: 4410 sheet: 1.19 (0.15), residues: 1188 loop : -0.18 (0.13), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 483 HIS 0.007 0.001 HIS D 126 PHE 0.004 0.001 PHE J 489 TYR 0.017 0.002 TYR M 26 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 782 time to evaluate : 5.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8472 (ptt) cc_final: 0.8216 (ptm) REVERT: A 57 MET cc_start: 0.8685 (ppp) cc_final: 0.8213 (ppp) REVERT: A 455 MET cc_start: 0.8412 (tmm) cc_final: 0.8205 (tmm) REVERT: B 90 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8940 (tm-30) REVERT: B 455 MET cc_start: 0.8408 (tmm) cc_final: 0.8189 (tmm) REVERT: B 526 ASP cc_start: 0.8283 (t0) cc_final: 0.7555 (t0) REVERT: C 90 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8951 (tm-30) REVERT: C 455 MET cc_start: 0.8509 (tmm) cc_final: 0.8078 (tmm) REVERT: C 487 ASN cc_start: 0.7159 (t0) cc_final: 0.6877 (t0) REVERT: C 526 ASP cc_start: 0.8628 (t0) cc_final: 0.8109 (t70) REVERT: C 527 ASP cc_start: 0.6688 (m-30) cc_final: 0.6266 (m-30) REVERT: D 90 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8920 (tm-30) REVERT: D 455 MET cc_start: 0.8442 (tmm) cc_final: 0.8197 (tmm) REVERT: D 487 ASN cc_start: 0.7691 (t0) cc_final: 0.7161 (t0) REVERT: E 54 MET cc_start: 0.8486 (ppp) cc_final: 0.8286 (ppp) REVERT: E 90 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9023 (tm-30) REVERT: E 455 MET cc_start: 0.8527 (tmm) cc_final: 0.8201 (tmm) REVERT: E 471 GLN cc_start: 0.9218 (tt0) cc_final: 0.8959 (tt0) REVERT: E 494 GLU cc_start: 0.7599 (mp0) cc_final: 0.7114 (mp0) REVERT: E 526 ASP cc_start: 0.7885 (t0) cc_final: 0.7370 (t70) REVERT: F 57 MET cc_start: 0.8627 (ppp) cc_final: 0.7854 (ppp) REVERT: F 90 GLN cc_start: 0.9264 (tm-30) cc_final: 0.9016 (tm-30) REVERT: F 455 MET cc_start: 0.8522 (tmm) cc_final: 0.8243 (tmm) REVERT: F 487 ASN cc_start: 0.7532 (t0) cc_final: 0.6981 (t0) REVERT: G 49 TYR cc_start: 0.8134 (t80) cc_final: 0.7722 (t80) REVERT: G 54 MET cc_start: 0.8155 (ptm) cc_final: 0.7781 (ptm) REVERT: G 87 LEU cc_start: 0.9307 (tp) cc_final: 0.9034 (pp) REVERT: G 90 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9034 (tm-30) REVERT: G 455 MET cc_start: 0.8580 (tmm) cc_final: 0.8262 (tmm) REVERT: G 471 GLN cc_start: 0.9253 (tt0) cc_final: 0.9017 (tt0) REVERT: G 521 LEU cc_start: 0.9192 (tp) cc_final: 0.8934 (tt) REVERT: G 527 ASP cc_start: 0.6665 (m-30) cc_final: 0.6442 (m-30) REVERT: H 49 TYR cc_start: 0.8037 (t80) cc_final: 0.7560 (t80) REVERT: H 54 MET cc_start: 0.8451 (ptt) cc_final: 0.8229 (ptm) REVERT: H 90 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8946 (tm-30) REVERT: H 455 MET cc_start: 0.8541 (tmm) cc_final: 0.8160 (tmm) REVERT: H 487 ASN cc_start: 0.7498 (t0) cc_final: 0.6910 (t0) REVERT: H 494 GLU cc_start: 0.7809 (mp0) cc_final: 0.7342 (mp0) REVERT: H 521 LEU cc_start: 0.9345 (tp) cc_final: 0.9079 (tt) REVERT: H 526 ASP cc_start: 0.8545 (t0) cc_final: 0.7837 (t70) REVERT: I 455 MET cc_start: 0.8530 (tmm) cc_final: 0.8116 (tmm) REVERT: I 487 ASN cc_start: 0.7011 (t0) cc_final: 0.6127 (t0) REVERT: I 521 LEU cc_start: 0.9400 (tp) cc_final: 0.9146 (tt) REVERT: J 49 TYR cc_start: 0.8046 (t80) cc_final: 0.7845 (t80) REVERT: J 455 MET cc_start: 0.8452 (tmm) cc_final: 0.8211 (tmm) REVERT: J 487 ASN cc_start: 0.7636 (t0) cc_final: 0.7099 (t0) REVERT: K 49 TYR cc_start: 0.8092 (t80) cc_final: 0.7879 (t80) REVERT: K 90 GLN cc_start: 0.9272 (tm-30) cc_final: 0.9018 (tm-30) REVERT: K 455 MET cc_start: 0.8541 (tmm) cc_final: 0.8231 (tmm) REVERT: K 471 GLN cc_start: 0.9225 (tt0) cc_final: 0.8968 (tt0) REVERT: K 494 GLU cc_start: 0.7603 (mp0) cc_final: 0.7123 (mp0) REVERT: K 526 ASP cc_start: 0.7933 (t0) cc_final: 0.7644 (t0) REVERT: L 54 MET cc_start: 0.8559 (ptp) cc_final: 0.7647 (ptm) REVERT: L 57 MET cc_start: 0.8648 (ppp) cc_final: 0.8108 (ppp) REVERT: L 90 GLN cc_start: 0.9260 (tm-30) cc_final: 0.9001 (tm-30) REVERT: L 455 MET cc_start: 0.8501 (tmm) cc_final: 0.8228 (tmm) REVERT: L 487 ASN cc_start: 0.7534 (t0) cc_final: 0.6983 (t0) REVERT: M 49 TYR cc_start: 0.8139 (t80) cc_final: 0.7719 (t80) REVERT: M 54 MET cc_start: 0.8135 (ptm) cc_final: 0.7760 (ptm) REVERT: M 87 LEU cc_start: 0.9306 (tp) cc_final: 0.9038 (pp) REVERT: M 90 GLN cc_start: 0.9291 (tm-30) cc_final: 0.9031 (tm-30) REVERT: M 455 MET cc_start: 0.8596 (tmm) cc_final: 0.8268 (tmm) REVERT: M 521 LEU cc_start: 0.9186 (tp) cc_final: 0.8920 (tt) REVERT: M 526 ASP cc_start: 0.8253 (t0) cc_final: 0.7537 (t70) REVERT: N 49 TYR cc_start: 0.8035 (t80) cc_final: 0.7531 (t80) REVERT: N 54 MET cc_start: 0.8353 (ptt) cc_final: 0.7986 (ptt) REVERT: N 90 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8953 (tm-30) REVERT: N 455 MET cc_start: 0.8536 (tmm) cc_final: 0.8158 (tmm) REVERT: N 487 ASN cc_start: 0.7495 (t0) cc_final: 0.6899 (t0) REVERT: N 494 GLU cc_start: 0.7795 (mp0) cc_final: 0.7337 (mp0) REVERT: N 521 LEU cc_start: 0.9352 (tp) cc_final: 0.9080 (tt) REVERT: N 526 ASP cc_start: 0.8568 (t0) cc_final: 0.7876 (t70) REVERT: O 90 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9046 (tm-30) REVERT: O 455 MET cc_start: 0.8461 (tmm) cc_final: 0.8117 (tmm) REVERT: O 470 MET cc_start: 0.8345 (tpp) cc_final: 0.8064 (tpp) REVERT: O 487 ASN cc_start: 0.7385 (t0) cc_final: 0.6948 (t0) REVERT: O 494 GLU cc_start: 0.8446 (pm20) cc_final: 0.7780 (pm20) REVERT: O 521 LEU cc_start: 0.9432 (tp) cc_final: 0.9191 (tt) REVERT: O 526 ASP cc_start: 0.8327 (t0) cc_final: 0.7307 (t0) REVERT: P 54 MET cc_start: 0.8482 (ptt) cc_final: 0.8222 (ptm) REVERT: P 57 MET cc_start: 0.8682 (ppp) cc_final: 0.8215 (ppp) REVERT: P 455 MET cc_start: 0.8404 (tmm) cc_final: 0.8192 (tmm) REVERT: Q 90 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8926 (tm-30) REVERT: Q 201 VAL cc_start: 0.8817 (t) cc_final: 0.8421 (t) REVERT: Q 455 MET cc_start: 0.8385 (tmm) cc_final: 0.8181 (tmm) REVERT: Q 526 ASP cc_start: 0.8282 (t0) cc_final: 0.7560 (t0) REVERT: R 90 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8946 (tm-30) REVERT: R 455 MET cc_start: 0.8506 (tmm) cc_final: 0.8097 (tmm) REVERT: R 526 ASP cc_start: 0.8630 (t0) cc_final: 0.8108 (t70) REVERT: R 527 ASP cc_start: 0.6716 (m-30) cc_final: 0.6295 (m-30) outliers start: 2 outliers final: 0 residues processed: 782 average time/residue: 0.4976 time to fit residues: 678.4245 Evaluate side-chains 516 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 757 optimal weight: 1.9990 chunk 498 optimal weight: 50.0000 chunk 803 optimal weight: 6.9990 chunk 490 optimal weight: 9.9990 chunk 381 optimal weight: 8.9990 chunk 558 optimal weight: 4.9990 chunk 842 optimal weight: 1.9990 chunk 775 optimal weight: 9.9990 chunk 671 optimal weight: 0.0570 chunk 69 optimal weight: 50.0000 chunk 518 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 460 ASN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58968 Z= 0.207 Angle : 0.591 6.872 80172 Z= 0.297 Chirality : 0.042 0.182 9954 Planarity : 0.004 0.057 10386 Dihedral : 5.271 58.669 9000 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.16 (0.09), residues: 8226 helix: 1.21 (0.08), residues: 4410 sheet: 1.47 (0.15), residues: 1134 loop : -0.17 (0.13), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 483 HIS 0.003 0.001 HIS P 126 PHE 0.004 0.001 PHE N 489 TYR 0.015 0.001 TYR L 26 ARG 0.008 0.000 ARG F 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16452 Ramachandran restraints generated. 8226 Oldfield, 0 Emsley, 8226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 752 time to evaluate : 6.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8687 (ppp) cc_final: 0.8257 (ppp) REVERT: A 455 MET cc_start: 0.8415 (tmm) cc_final: 0.8210 (tmm) REVERT: A 471 GLN cc_start: 0.9182 (tt0) cc_final: 0.8975 (tt0) REVERT: A 482 LYS cc_start: 0.8696 (tttt) cc_final: 0.8455 (tttt) REVERT: B 90 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 58 LEU cc_start: 0.8627 (mm) cc_final: 0.8382 (mm) REVERT: C 90 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8958 (tm-30) REVERT: C 455 MET cc_start: 0.8498 (tmm) cc_final: 0.8049 (tmm) REVERT: C 487 ASN cc_start: 0.7280 (t0) cc_final: 0.7038 (t0) REVERT: C 526 ASP cc_start: 0.8422 (t0) cc_final: 0.8210 (t70) REVERT: C 527 ASP cc_start: 0.6456 (m-30) cc_final: 0.6179 (m-30) REVERT: D 90 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8908 (tm-30) REVERT: D 104 LYS cc_start: 0.8812 (mppt) cc_final: 0.8527 (mttt) REVERT: D 455 MET cc_start: 0.8404 (tmm) cc_final: 0.8084 (tmm) REVERT: E 49 TYR cc_start: 0.7729 (t80) cc_final: 0.7484 (t80) REVERT: E 54 MET cc_start: 0.8414 (ppp) cc_final: 0.8208 (ppp) REVERT: E 455 MET cc_start: 0.8499 (tmm) cc_final: 0.8166 (tmm) REVERT: E 471 GLN cc_start: 0.9227 (tt0) cc_final: 0.8960 (tt0) REVERT: E 494 GLU cc_start: 0.7624 (mp0) cc_final: 0.7141 (mp0) REVERT: E 526 ASP cc_start: 0.7992 (t0) cc_final: 0.7288 (t70) REVERT: F 54 MET cc_start: 0.8274 (ptm) cc_final: 0.7677 (ptm) REVERT: F 57 MET cc_start: 0.8853 (ppp) cc_final: 0.8051 (ppp) REVERT: F 90 GLN cc_start: 0.9271 (tm-30) cc_final: 0.9021 (tm-30) REVERT: F 455 MET cc_start: 0.8497 (tmm) cc_final: 0.8199 (tmm) REVERT: F 487 ASN cc_start: 0.7464 (t0) cc_final: 0.6922 (t0) REVERT: G 49 TYR cc_start: 0.8079 (t80) cc_final: 0.7693 (t80) REVERT: G 55 ASP cc_start: 0.8387 (m-30) cc_final: 0.7966 (m-30) REVERT: G 87 LEU cc_start: 0.9316 (tp) cc_final: 0.9038 (pp) REVERT: G 90 GLN cc_start: 0.9303 (tm-30) cc_final: 0.9018 (tm-30) REVERT: G 112 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7812 (mm-30) REVERT: G 455 MET cc_start: 0.8565 (tmm) cc_final: 0.8260 (tmm) REVERT: G 471 GLN cc_start: 0.9246 (tt0) cc_final: 0.8992 (tt0) REVERT: G 521 LEU cc_start: 0.9183 (tp) cc_final: 0.8943 (tt) REVERT: G 526 ASP cc_start: 0.8424 (t0) cc_final: 0.8189 (t70) REVERT: H 49 TYR cc_start: 0.8008 (t80) cc_final: 0.7535 (t80) REVERT: H 57 MET cc_start: 0.8660 (ppp) cc_final: 0.8099 (ppp) REVERT: H 90 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8935 (tm-30) REVERT: H 104 LYS cc_start: 0.8395 (pttm) cc_final: 0.8170 (pttm) REVERT: H 455 MET cc_start: 0.8557 (tmm) cc_final: 0.8146 (tmm) REVERT: H 487 ASN cc_start: 0.7374 (t0) cc_final: 0.6867 (t0) REVERT: H 494 GLU cc_start: 0.7762 (mp0) cc_final: 0.7421 (mp0) REVERT: H 521 LEU cc_start: 0.9312 (tp) cc_final: 0.9045 (tt) REVERT: I 87 LEU cc_start: 0.9354 (pp) cc_final: 0.9140 (tp) REVERT: I 455 MET cc_start: 0.8525 (tmm) cc_final: 0.8132 (tmm) REVERT: I 470 MET cc_start: 0.8408 (tpp) cc_final: 0.8109 (tpp) REVERT: I 487 ASN cc_start: 0.7139 (t0) cc_final: 0.6819 (t0) REVERT: J 49 TYR cc_start: 0.8112 (t80) cc_final: 0.7878 (t80) REVERT: J 104 LYS cc_start: 0.8828 (mppt) cc_final: 0.8524 (mttt) REVERT: J 455 MET cc_start: 0.8402 (tmm) cc_final: 0.8094 (tmm) REVERT: J 487 ASN cc_start: 0.7556 (t0) cc_final: 0.7037 (t0) REVERT: K 455 MET cc_start: 0.8543 (tmm) cc_final: 0.8193 (tmm) REVERT: K 471 GLN cc_start: 0.9238 (tt0) cc_final: 0.8964 (tt0) REVERT: K 494 GLU cc_start: 0.7624 (mp0) cc_final: 0.7142 (mp0) REVERT: L 57 MET cc_start: 0.8817 (ppp) cc_final: 0.8144 (ppp) REVERT: L 90 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8994 (tm-30) REVERT: L 455 MET cc_start: 0.8469 (tmm) cc_final: 0.8195 (tmm) REVERT: M 49 TYR cc_start: 0.8089 (t80) cc_final: 0.7696 (t80) REVERT: M 55 ASP cc_start: 0.8388 (m-30) cc_final: 0.7941 (m-30) REVERT: M 57 MET cc_start: 0.8811 (ppp) cc_final: 0.8593 (ppp) REVERT: M 87 LEU cc_start: 0.9325 (tp) cc_final: 0.9044 (pp) REVERT: M 90 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9016 (tm-30) REVERT: M 112 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7817 (mm-30) REVERT: M 455 MET cc_start: 0.8569 (tmm) cc_final: 0.8272 (tmm) REVERT: M 521 LEU cc_start: 0.9162 (tp) cc_final: 0.8910 (tt) REVERT: N 49 TYR cc_start: 0.8019 (t80) cc_final: 0.7541 (t80) REVERT: N 54 MET cc_start: 0.8312 (ptt) cc_final: 0.7957 (ptt) REVERT: N 90 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8939 (tm-30) REVERT: N 104 LYS cc_start: 0.8390 (pttm) cc_final: 0.8172 (pttm) REVERT: N 455 MET cc_start: 0.8544 (tmm) cc_final: 0.8141 (tmm) REVERT: N 487 ASN cc_start: 0.7364 (t0) cc_final: 0.6848 (t0) REVERT: N 494 GLU cc_start: 0.7751 (mp0) cc_final: 0.7418 (mp0) REVERT: N 521 LEU cc_start: 0.9316 (tp) cc_final: 0.9050 (tt) REVERT: O 54 MET cc_start: 0.8206 (ppp) cc_final: 0.7715 (ppp) REVERT: O 90 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9033 (tm-30) REVERT: O 455 MET cc_start: 0.8478 (tmm) cc_final: 0.8135 (tmm) REVERT: O 470 MET cc_start: 0.8363 (tpp) cc_final: 0.8097 (tpp) REVERT: O 487 ASN cc_start: 0.7143 (t0) cc_final: 0.6917 (t0) REVERT: O 494 GLU cc_start: 0.8429 (pm20) cc_final: 0.7704 (pm20) REVERT: O 521 LEU cc_start: 0.9409 (tp) cc_final: 0.9164 (tt) REVERT: O 526 ASP cc_start: 0.8292 (t0) cc_final: 0.7149 (t0) REVERT: P 57 MET cc_start: 0.8685 (ppp) cc_final: 0.8254 (ppp) REVERT: P 455 MET cc_start: 0.8407 (tmm) cc_final: 0.8206 (tmm) REVERT: P 471 GLN cc_start: 0.9175 (tt0) cc_final: 0.8959 (tt0) REVERT: P 482 LYS cc_start: 0.8703 (tttt) cc_final: 0.8464 (tttt) REVERT: Q 455 MET cc_start: 0.8382 (tmm) cc_final: 0.8155 (tmm) REVERT: R 90 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8966 (tm-30) REVERT: R 455 MET cc_start: 0.8500 (tmm) cc_final: 0.8051 (tmm) REVERT: R 526 ASP cc_start: 0.8424 (t0) cc_final: 0.7987 (t70) outliers start: 0 outliers final: 0 residues processed: 752 average time/residue: 0.4846 time to fit residues: 643.5049 Evaluate side-chains 556 residues out of total 6804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 411 optimal weight: 0.0030 chunk 533 optimal weight: 0.9980 chunk 714 optimal weight: 1.9990 chunk 205 optimal weight: 0.0050 chunk 618 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 672 optimal weight: 0.3980 chunk 281 optimal weight: 4.9990 chunk 690 optimal weight: 50.0000 chunk 85 optimal weight: 3.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 460 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 460 ASN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.114514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075663 restraints weight = 172994.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076703 restraints weight = 107250.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077843 restraints weight = 72309.893| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 58968 Z= 0.129 Angle : 0.558 7.313 80172 Z= 0.274 Chirality : 0.040 0.182 9954 Planarity : 0.003 0.056 10386 Dihedral : 4.909 55.555 9000 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.47 (0.10), residues: 8226 helix: 1.51 (0.08), residues: 4428 sheet: 1.66 (0.16), residues: 1134 loop : -0.16 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 199 HIS 0.002 0.000 HIS J 476 PHE 0.003 0.001 PHE R 489 TYR 0.011 0.001 TYR Q 200 ARG 0.023 0.000 ARG M 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13052.65 seconds wall clock time: 229 minutes 26.52 seconds (13766.52 seconds total)