Starting phenix.real_space_refine on Sat Apr 6 21:29:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x35_22018/04_2024/6x35_22018_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Zn 4 6.06 5 S 684 5.16 5 C 71588 2.51 5 N 19896 2.21 5 O 19716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 71": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B ARG 1110": "NH1" <-> "NH2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1290": "NH1" <-> "NH2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1618": "NH1" <-> "NH2" Residue "B ARG 1619": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B ARG 1798": "NH1" <-> "NH2" Residue "B ARG 1828": "NH1" <-> "NH2" Residue "B ARG 2000": "NH1" <-> "NH2" Residue "B ARG 2141": "NH1" <-> "NH2" Residue "B ARG 2356": "NH1" <-> "NH2" Residue "B ARG 2453": "NH1" <-> "NH2" Residue "B ARG 2455": "NH1" <-> "NH2" Residue "B ARG 2553": "NH1" <-> "NH2" Residue "B ARG 2613": "NH1" <-> "NH2" Residue "B ARG 2616": "NH1" <-> "NH2" Residue "B ARG 3437": "NH1" <-> "NH2" Residue "B ARG 3644": "NH1" <-> "NH2" Residue "B ARG 3881": "NH1" <-> "NH2" Residue "B ARG 3899": "NH1" <-> "NH2" Residue "B ARG 3979": "NH1" <-> "NH2" Residue "B ARG 4037": "NH1" <-> "NH2" Residue "B ARG 4126": "NH1" <-> "NH2" Residue "B ARG 4132": "NH1" <-> "NH2" Residue "B ARG 4154": "NH1" <-> "NH2" Residue "B ARG 4170": "NH1" <-> "NH2" Residue "B ARG 4187": "NH1" <-> "NH2" Residue "B ARG 4555": "NH1" <-> "NH2" Residue "B ARG 4671": "NH1" <-> "NH2" Residue "B ARG 4701": "NH1" <-> "NH2" Residue "B ARG 4720": "NH1" <-> "NH2" Residue "B ARG 4734": "NH1" <-> "NH2" Residue "B ARG 4822": "NH1" <-> "NH2" Residue "B ARG 4858": "NH1" <-> "NH2" Residue "B TYR 4886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4911": "NH1" <-> "NH2" Residue "B ARG 4949": "NH1" <-> "NH2" Residue "B ARG 5027": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E ARG 474": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E ARG 683": "NH1" <-> "NH2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E ARG 1110": "NH1" <-> "NH2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1290": "NH1" <-> "NH2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1618": "NH1" <-> "NH2" Residue "E ARG 1619": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E ARG 1798": "NH1" <-> "NH2" Residue "E ARG 1828": "NH1" <-> "NH2" Residue "E ARG 2000": "NH1" <-> "NH2" Residue "E ARG 2141": "NH1" <-> "NH2" Residue "E ARG 2356": "NH1" <-> "NH2" Residue "E ARG 2453": "NH1" <-> "NH2" Residue "E ARG 2455": "NH1" <-> "NH2" Residue "E ARG 2553": "NH1" <-> "NH2" Residue "E ARG 2613": "NH1" <-> "NH2" Residue "E ARG 2616": "NH1" <-> "NH2" Residue "E ARG 3437": "NH1" <-> "NH2" Residue "E ARG 3644": "NH1" <-> "NH2" Residue "E ARG 3881": "NH1" <-> "NH2" Residue "E ARG 3899": "NH1" <-> "NH2" Residue "E ARG 3979": "NH1" <-> "NH2" Residue "E ARG 4037": "NH1" <-> "NH2" Residue "E ARG 4126": "NH1" <-> "NH2" Residue "E ARG 4132": "NH1" <-> "NH2" Residue "E ARG 4154": "NH1" <-> "NH2" Residue "E ARG 4170": "NH1" <-> "NH2" Residue "E ARG 4187": "NH1" <-> "NH2" Residue "E ARG 4555": "NH1" <-> "NH2" Residue "E ARG 4671": "NH1" <-> "NH2" Residue "E ARG 4701": "NH1" <-> "NH2" Residue "E ARG 4720": "NH1" <-> "NH2" Residue "E ARG 4734": "NH1" <-> "NH2" Residue "E ARG 4822": "NH1" <-> "NH2" Residue "E ARG 4858": "NH1" <-> "NH2" Residue "E TYR 4886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4911": "NH1" <-> "NH2" Residue "E ARG 4949": "NH1" <-> "NH2" Residue "E ARG 5027": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H ARG 426": "NH1" <-> "NH2" Residue "H ARG 469": "NH1" <-> "NH2" Residue "H ARG 474": "NH1" <-> "NH2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ARG 844": "NH1" <-> "NH2" Residue "H ARG 1110": "NH1" <-> "NH2" Residue "H ARG 1271": "NH1" <-> "NH2" Residue "H ARG 1290": "NH1" <-> "NH2" Residue "H ARG 1594": "NH1" <-> "NH2" Residue "H ARG 1607": "NH1" <-> "NH2" Residue "H ARG 1618": "NH1" <-> "NH2" Residue "H ARG 1619": "NH1" <-> "NH2" Residue "H ARG 1656": "NH1" <-> "NH2" Residue "H ARG 1725": "NH1" <-> "NH2" Residue "H ARG 1743": "NH1" <-> "NH2" Residue "H ARG 1798": "NH1" <-> "NH2" Residue "H ARG 1828": "NH1" <-> "NH2" Residue "H ARG 2000": "NH1" <-> "NH2" Residue "H ARG 2141": "NH1" <-> "NH2" Residue "H ARG 2356": "NH1" <-> "NH2" Residue "H ARG 2453": "NH1" <-> "NH2" Residue "H ARG 2455": "NH1" <-> "NH2" Residue "H ARG 2553": "NH1" <-> "NH2" Residue "H ARG 2613": "NH1" <-> "NH2" Residue "H ARG 2616": "NH1" <-> "NH2" Residue "H ARG 3437": "NH1" <-> "NH2" Residue "H ARG 3644": "NH1" <-> "NH2" Residue "H ARG 3881": "NH1" <-> "NH2" Residue "H ARG 3899": "NH1" <-> "NH2" Residue "H ARG 3979": "NH1" <-> "NH2" Residue "H ARG 4037": "NH1" <-> "NH2" Residue "H ARG 4126": "NH1" <-> "NH2" Residue "H ARG 4132": "NH1" <-> "NH2" Residue "H ARG 4154": "NH1" <-> "NH2" Residue "H ARG 4170": "NH1" <-> "NH2" Residue "H ARG 4187": "NH1" <-> "NH2" Residue "H ARG 4555": "NH1" <-> "NH2" Residue "H ARG 4671": "NH1" <-> "NH2" Residue "H ARG 4701": "NH1" <-> "NH2" Residue "H ARG 4720": "NH1" <-> "NH2" Residue "H ARG 4734": "NH1" <-> "NH2" Residue "H ARG 4822": "NH1" <-> "NH2" Residue "H ARG 4858": "NH1" <-> "NH2" Residue "H TYR 4886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4911": "NH1" <-> "NH2" Residue "H ARG 4949": "NH1" <-> "NH2" Residue "H ARG 5027": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 125": "NH1" <-> "NH2" Residue "K ARG 178": "NH1" <-> "NH2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K ARG 426": "NH1" <-> "NH2" Residue "K ARG 469": "NH1" <-> "NH2" Residue "K ARG 474": "NH1" <-> "NH2" Residue "K ARG 553": "NH1" <-> "NH2" Residue "K ARG 683": "NH1" <-> "NH2" Residue "K ARG 844": "NH1" <-> "NH2" Residue "K ARG 1110": "NH1" <-> "NH2" Residue "K ARG 1271": "NH1" <-> "NH2" Residue "K ARG 1290": "NH1" <-> "NH2" Residue "K ARG 1594": "NH1" <-> "NH2" Residue "K ARG 1607": "NH1" <-> "NH2" Residue "K ARG 1618": "NH1" <-> "NH2" Residue "K ARG 1619": "NH1" <-> "NH2" Residue "K ARG 1656": "NH1" <-> "NH2" Residue "K ARG 1725": "NH1" <-> "NH2" Residue "K ARG 1743": "NH1" <-> "NH2" Residue "K ARG 1798": "NH1" <-> "NH2" Residue "K ARG 1828": "NH1" <-> "NH2" Residue "K ARG 2000": "NH1" <-> "NH2" Residue "K ARG 2141": "NH1" <-> "NH2" Residue "K ARG 2356": "NH1" <-> "NH2" Residue "K ARG 2453": "NH1" <-> "NH2" Residue "K ARG 2455": "NH1" <-> "NH2" Residue "K ARG 2553": "NH1" <-> "NH2" Residue "K ARG 2613": "NH1" <-> "NH2" Residue "K ARG 2616": "NH1" <-> "NH2" Residue "K ARG 3437": "NH1" <-> "NH2" Residue "K ARG 3644": "NH1" <-> "NH2" Residue "K ARG 3881": "NH1" <-> "NH2" Residue "K ARG 3899": "NH1" <-> "NH2" Residue "K ARG 3979": "NH1" <-> "NH2" Residue "K ARG 4037": "NH1" <-> "NH2" Residue "K ARG 4126": "NH1" <-> "NH2" Residue "K ARG 4132": "NH1" <-> "NH2" Residue "K ARG 4154": "NH1" <-> "NH2" Residue "K ARG 4170": "NH1" <-> "NH2" Residue "K ARG 4187": "NH1" <-> "NH2" Residue "K ARG 4555": "NH1" <-> "NH2" Residue "K ARG 4671": "NH1" <-> "NH2" Residue "K ARG 4701": "NH1" <-> "NH2" Residue "K ARG 4720": "NH1" <-> "NH2" Residue "K ARG 4734": "NH1" <-> "NH2" Residue "K ARG 4822": "NH1" <-> "NH2" Residue "K ARG 4858": "NH1" <-> "NH2" Residue "K TYR 4886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 4911": "NH1" <-> "NH2" Residue "K ARG 4949": "NH1" <-> "NH2" Residue "K ARG 5027": "NH1" <-> "NH2" Residue "L ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 111888 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 740 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 26463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 Conformer: "B" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 bond proxies already assigned to first conformer: 26923 Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 768 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 740 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 26463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 Conformer: "B" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 bond proxies already assigned to first conformer: 26923 Chain: "F" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 768 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "G" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 740 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 26463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 Conformer: "B" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 bond proxies already assigned to first conformer: 26923 Chain: "I" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 768 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "J" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 740 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "K" Number of atoms: 26463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 Conformer: "B" Number of residues, atoms: 3801, 26448 Classifications: {'peptide': 3801} Incomplete info: {'truncation_to_alanine': 1159} Link IDs: {'PTRANS': 156, 'TRANS': 3644} Chain breaks: 57 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3754 Unresolved non-hydrogen angles: 4875 Unresolved non-hydrogen dihedrals: 2833 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 46, 'UNK:plan-1': 357, 'ASP:plan': 103, 'TYR:plan': 16, 'ASN:plan1': 37, 'TRP:plan': 9, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 202, 'ARG:plan': 64} Unresolved non-hydrogen planarities: 2461 bond proxies already assigned to first conformer: 26923 Chain: "L" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 768 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26587 SG CYS B4956 147.045 173.024 81.823 1.00160.39 S ATOM 54558 SG CYS E4956 129.996 147.045 81.823 1.00160.39 S ATOM 82529 SG CYS H4956 155.974 129.997 81.823 1.00160.39 S ATOM A083O SG CYS K4956 173.023 155.976 81.823 1.00160.39 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALYS B2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS B2750 " occ=0.50 residue: pdb=" N ALYS E2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS E2750 " occ=0.50 residue: pdb=" N ALYS H2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS H2750 " occ=0.50 residue: pdb=" N ALYS K2750 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS K2750 " occ=0.50 Time building chain proxies: 79.82, per 1000 atoms: 0.71 Number of scatterers: 111888 At special positions: 0 Unit cell: (304.11, 304.11, 202.74, 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) Zn 4 29.99 S 684 16.00 O 19716 8.00 N 19896 7.00 C 71588 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: 31.68 Conformation dependent library (CDL) restraints added in 28.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4956 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4976 " pdb=" ZN E5101 " pdb="ZN ZN E5101 " - pdb=" ND1 HIS E4981 " pdb="ZN ZN E5101 " - pdb=" SG CYS E4956 " pdb="ZN ZN E5101 " - pdb=" NE2 HIS E4976 " pdb=" ZN H5101 " pdb="ZN ZN H5101 " - pdb=" ND1 HIS H4981 " pdb="ZN ZN H5101 " - pdb=" SG CYS H4956 " pdb="ZN ZN H5101 " - pdb=" NE2 HIS H4976 " pdb=" ZN K5101 " pdb="ZN ZN K5101 " - pdb=" ND1 HIS K4981 " pdb="ZN ZN K5101 " - pdb=" SG CYS K4956 " pdb="ZN ZN K5101 " - pdb=" NE2 HIS K4976 " 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30536 Finding SS restraints... Secondary structure from input PDB file: 620 helices and 108 sheets defined 61.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.94 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.405A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 66 Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.537A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 255 through 258 removed outlier: 4.171A pdb=" N SER B 258 " --> pdb=" O HIS B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.607A pdb=" N SER B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 Processing helix chain 'B' and resid 460 through 481 Processing helix chain 'B' and resid 482 through 495 removed outlier: 3.898A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 511 through 531 removed outlier: 4.202A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.682A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.833A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.715A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 608 removed outlier: 3.964A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 812 through 815 removed outlier: 3.795A pdb=" N VAL B 815 " --> pdb=" O HIS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 864 through 889 Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 943 through 949 Processing helix chain 'B' and resid 955 through 960 removed outlier: 4.004A pdb=" N TYR B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 955 through 960' Processing helix chain 'B' and resid 978 through 1004 Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 4.216A pdb=" N VAL B1022 " --> pdb=" O PRO B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 3.535A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1222 removed outlier: 3.928A pdb=" N CYS B1217 " --> pdb=" O PHE B1213 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN B1220 " --> pdb=" O ILE B1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1446 No H-bonds generated for 'chain 'B' and resid 1444 through 1446' Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 3.590A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1654 Processing helix chain 'B' and resid 1657 through 1674 removed outlier: 4.104A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1679 through 1689 removed outlier: 3.517A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 3.575A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1721 through 1731 Processing helix chain 'B' and resid 1739 through 1744 removed outlier: 3.521A pdb=" N ALA B1744 " --> pdb=" O PRO B1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1826 removed outlier: 3.639A pdb=" N GLN B1825 " --> pdb=" O ARG B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1853 Proline residue: B1841 - end of helix removed outlier: 3.671A pdb=" N MET B1852 " --> pdb=" O THR B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1868 removed outlier: 3.591A pdb=" N VAL B1860 " --> pdb=" O GLY B1856 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B1861 " --> pdb=" O ASP B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1983 removed outlier: 3.690A pdb=" N LYS B1937 " --> pdb=" O PRO B1933 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B1938 " --> pdb=" O GLU B1934 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN B1939 " --> pdb=" O SER B1935 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B1969 " --> pdb=" O ARG B1965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2001 removed outlier: 4.562A pdb=" N GLU B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B1999 " --> pdb=" O ARG B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2011 Processing helix chain 'B' and resid 2028 through 2044 removed outlier: 3.777A pdb=" N LEU B2032 " --> pdb=" O ILE B2028 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B2044 " --> pdb=" O LEU B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 removed outlier: 4.382A pdb=" N ASP B2110 " --> pdb=" O TRP B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2130 Processing helix chain 'B' and resid 2130 through 2139 removed outlier: 3.564A pdb=" N GLU B2134 " --> pdb=" O ASP B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2168 removed outlier: 4.017A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2187 Processing helix chain 'B' and resid 2188 through 2189 No H-bonds generated for 'chain 'B' and resid 2188 through 2189' Processing helix chain 'B' and resid 2190 through 2194 Processing helix chain 'B' and resid 2195 through 2203 removed outlier: 4.003A pdb=" N MET B2199 " --> pdb=" O HIS B2195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B2200 " --> pdb=" O PRO B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 Processing helix chain 'B' and resid 2226 through 2242 removed outlier: 3.585A pdb=" N ARG B2242 " --> pdb=" O CYS B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2244 through 2253 Processing helix chain 'B' and resid 2254 through 2263 removed outlier: 3.581A pdb=" N LEU B2258 " --> pdb=" O HIS B2254 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 Processing helix chain 'B' and resid 2284 through 2290 removed outlier: 3.609A pdb=" N ALA B2288 " --> pdb=" O ASN B2284 " (cutoff:3.500A) Processing helix chain 'B' and resid 2292 through 2307 removed outlier: 3.934A pdb=" N LEU B2296 " --> pdb=" O GLN B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 Processing helix chain 'B' and resid 2325 through 2340 removed outlier: 3.851A pdb=" N GLY B2329 " --> pdb=" O ASN B2325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B2331 " --> pdb=" O CYS B2327 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2361 removed outlier: 3.892A pdb=" N LYS B2361 " --> pdb=" O LEU B2357 " (cutoff:3.500A) Processing helix chain 'B' and resid 2362 through 2365 Processing helix chain 'B' and resid 2378 through 2385 Processing helix chain 'B' and resid 2421 through 2437 Processing helix chain 'B' and resid 2448 through 2462 removed outlier: 3.685A pdb=" N LEU B2452 " --> pdb=" O LYS B2448 " (cutoff:3.500A) Processing helix chain 'B' and resid 2463 through 2472 removed outlier: 3.763A pdb=" N LEU B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2496 through 2511 removed outlier: 4.209A pdb=" N LYS B2500 " --> pdb=" O VAL B2496 " (cutoff:3.500A) Processing helix chain 'B' and resid 2519 through 2527 Processing helix chain 'B' and resid 2547 through 2566 removed outlier: 3.527A pdb=" N ALA B2558 " --> pdb=" O TYR B2554 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU B2560 " --> pdb=" O CYS B2556 " (cutoff:3.500A) Proline residue: B2561 - end of helix Processing helix chain 'B' and resid 2567 through 2570 Processing helix chain 'B' and resid 2580 through 2592 removed outlier: 3.520A pdb=" N ARG B2592 " --> pdb=" O TYR B2588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2597 through 2613 removed outlier: 3.641A pdb=" N ARG B2613 " --> pdb=" O MET B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2629 removed outlier: 3.521A pdb=" N LEU B2620 " --> pdb=" O ARG B2616 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B2623 " --> pdb=" O MET B2619 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B2625 " --> pdb=" O GLN B2621 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG B2626 " --> pdb=" O HIS B2622 " (cutoff:3.500A) Processing helix chain 'B' and resid 2642 through 2653 removed outlier: 4.198A pdb=" N UNK B2646 " --> pdb=" O UNK B2642 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N UNK B2651 " --> pdb=" O UNK B2647 " (cutoff:3.500A) Processing helix chain 'B' and resid 2665 through 2683 removed outlier: 3.513A pdb=" N UNK B2683 " --> pdb=" O UNK B2679 " (cutoff:3.500A) Processing helix chain 'B' and resid 2689 through 2700 Processing helix chain 'B' and resid 2750 through 2772 removed outlier: 4.500A pdb=" N PHE B2754 " --> pdb=" O ALYS B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2819 removed outlier: 3.676A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Proline residue: B2808 - end of helix Processing helix chain 'B' and resid 2868 through 2898 Processing helix chain 'B' and resid 2916 through 2933 removed outlier: 3.778A pdb=" N ASN B2933 " --> pdb=" O PHE B2929 " (cutoff:3.500A) Processing helix chain 'B' and resid 2957 through 2977 Processing helix chain 'B' and resid 3000 through 3018 Processing helix chain 'B' and resid 3033 through 3046 Processing helix chain 'B' and resid 3052 through 3062 Processing helix chain 'B' and resid 3144 through 3163 Processing helix chain 'B' and resid 3174 through 3193 Processing helix chain 'B' and resid 3203 through 3217 Processing helix chain 'B' and resid 3226 through 3238 Processing helix chain 'B' and resid 3279 through 3288 Processing helix chain 'B' and resid 3293 through 3308 Processing helix chain 'B' and resid 3321 through 3335 Processing helix chain 'B' and resid 3347 through 3358 Processing helix chain 'B' and resid 3366 through 3385 Processing helix chain 'B' and resid 3399 through 3427 Proline residue: B3411 - end of helix removed outlier: 6.068A pdb=" N ALA B3422 " --> pdb=" O ASP B3418 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS B3423 " --> pdb=" O ASN B3419 " (cutoff:3.500A) Processing helix chain 'B' and resid 3429 through 3449 Processing helix chain 'B' and resid 3449 through 3461 removed outlier: 3.533A pdb=" N LYS B3453 " --> pdb=" O SER B3449 " (cutoff:3.500A) Processing helix chain 'B' and resid 3510 through 3526 Processing helix chain 'B' and resid 3535 through 3544 Processing helix chain 'B' and resid 3549 through 3555 Processing helix chain 'B' and resid 3566 through 3574 Processing helix chain 'B' and resid 3587 through 3606 Processing helix chain 'B' and resid 3627 through 3632 removed outlier: 3.645A pdb=" N ALA B3630 " --> pdb=" O ALA B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3640 Processing helix chain 'B' and resid 3641 through 3657 removed outlier: 3.661A pdb=" N GLU B3651 " --> pdb=" O ASN B3647 " (cutoff:3.500A) Processing helix chain 'B' and resid 3665 through 3676 Processing helix chain 'B' and resid 3692 through 3708 removed outlier: 3.525A pdb=" N ALA B3705 " --> pdb=" O PHE B3701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B3706 " --> pdb=" O SER B3702 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B3707 " --> pdb=" O ARG B3703 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B3708 " --> pdb=" O THR B3704 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3730 removed outlier: 3.602A pdb=" N ASP B3723 " --> pdb=" O MET B3719 " (cutoff:3.500A) Processing helix chain 'B' and resid 3748 through 3767 removed outlier: 4.265A pdb=" N LEU B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3782 removed outlier: 4.166A pdb=" N MET B3773 " --> pdb=" O GLY B3769 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B3774 " --> pdb=" O ALA B3770 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B3775 " --> pdb=" O ALA B3771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B3778 " --> pdb=" O VAL B3774 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B3782 " --> pdb=" O ILE B3778 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3797 removed outlier: 3.749A pdb=" N SER B3790 " --> pdb=" O GLY B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3805 through 3819 removed outlier: 3.539A pdb=" N TYR B3814 " --> pdb=" O LYS B3810 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B3815 " --> pdb=" O MET B3811 " (cutoff:3.500A) Processing helix chain 'B' and resid 3822 through 3833 Processing helix chain 'B' and resid 3838 through 3850 removed outlier: 4.222A pdb=" N ARG B3844 " --> pdb=" O ASN B3840 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B3845 " --> pdb=" O ALA B3841 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B3846 " --> pdb=" O PHE B3842 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS B3847 " --> pdb=" O GLU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3872 through 3886 removed outlier: 3.632A pdb=" N THR B3876 " --> pdb=" O ASP B3872 " (cutoff:3.500A) Processing helix chain 'B' and resid 3891 through 3900 removed outlier: 3.854A pdb=" N GLN B3895 " --> pdb=" O ASN B3891 " (cutoff:3.500A) Processing helix chain 'B' and resid 3909 through 3932 removed outlier: 3.579A pdb=" N CYS B3913 " --> pdb=" O ASN B3909 " (cutoff:3.500A) Processing helix chain 'B' and resid 3941 through 3964 Processing helix chain 'B' and resid 3968 through 3977 removed outlier: 3.637A pdb=" N HIS B3977 " --> pdb=" O GLN B3973 " (cutoff:3.500A) Processing helix chain 'B' and resid 3979 through 3999 removed outlier: 3.674A pdb=" N HIS B3989 " --> pdb=" O VAL B3985 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B3990 " --> pdb=" O GLY B3986 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4026 removed outlier: 3.806A pdb=" N VAL B4020 " --> pdb=" O LYS B4016 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET B4021 " --> pdb=" O ASP B4017 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B4022 " --> pdb=" O MET B4018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B4023 " --> pdb=" O VAL B4019 " (cutoff:3.500A) Processing helix chain 'B' and resid 4033 through 4046 removed outlier: 4.358A pdb=" N ARG B4037 " --> pdb=" O GLY B4033 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B4046 " --> pdb=" O MET B4042 " (cutoff:3.500A) Processing helix chain 'B' and resid 4046 through 4069 removed outlier: 3.503A pdb=" N VAL B4050 " --> pdb=" O SER B4046 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B4063 " --> pdb=" O MET B4059 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B4064 " --> pdb=" O PHE B4060 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B4065 " --> pdb=" O LEU B4061 " (cutoff:3.500A) Processing helix chain 'B' and resid 4069 through 4075 removed outlier: 3.880A pdb=" N GLN B4073 " --> pdb=" O SER B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4123 through 4127 removed outlier: 3.560A pdb=" N ARG B4126 " --> pdb=" O PHE B4123 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B4127 " --> pdb=" O ALA B4124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4123 through 4127' Processing helix chain 'B' and resid 4128 through 4148 Processing helix chain 'B' and resid 4152 through 4167 removed outlier: 3.989A pdb=" N LEU B4161 " --> pdb=" O ASN B4157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B4165 " --> pdb=" O LEU B4161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B4167 " --> pdb=" O GLU B4163 " (cutoff:3.500A) Processing helix chain 'B' and resid 4168 through 4170 No H-bonds generated for 'chain 'B' and resid 4168 through 4170' Processing helix chain 'B' and resid 4193 through 4201 removed outlier: 3.553A pdb=" N ARG B4197 " --> pdb=" O SER B4193 " (cutoff:3.500A) Processing helix chain 'B' and resid 4202 through 4219 Processing helix chain 'B' and resid 4221 through 4241 removed outlier: 3.530A pdb=" N GLN B4241 " --> pdb=" O ILE B4237 " (cutoff:3.500A) Processing helix chain 'B' and resid 4316 through 4331 Processing helix chain 'B' and resid 4544 through 4576 removed outlier: 5.536A pdb=" N TYR B4558 " --> pdb=" O SER B4554 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR B4559 " --> pdb=" O ARG B4555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B4562 " --> pdb=" O TYR B4558 " (cutoff:3.500A) Processing helix chain 'B' and resid 4636 through 4682 removed outlier: 3.644A pdb=" N ALA B4640 " --> pdb=" O TYR B4636 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B4641 " --> pdb=" O MET B4637 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG B4642 " --> pdb=" O GLU B4638 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix Processing helix chain 'B' and resid 4694 through 4700 removed outlier: 3.681A pdb=" N GLN B4698 " --> pdb=" O ASP B4694 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4726 Processing helix chain 'B' and resid 4731 through 4737 Processing helix chain 'B' and resid 4762 through 4769 Processing helix chain 'B' and resid 4770 through 4783 removed outlier: 3.657A pdb=" N GLN B4774 " --> pdb=" O ASP B4770 " (cutoff:3.500A) Processing helix chain 'B' and resid 4784 through 4800 Processing helix chain 'B' and resid 4807 through 4815 removed outlier: 4.031A pdb=" N LEU B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B4812 " --> pdb=" O ALA B4808 " (cutoff:3.500A) Processing helix chain 'B' and resid 4818 through 4827 removed outlier: 3.696A pdb=" N THR B4823 " --> pdb=" O LYS B4819 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B4824 " --> pdb=" O THR B4820 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4857 removed outlier: 3.886A pdb=" N MET B4837 " --> pdb=" O LYS B4833 " (cutoff:3.500A) Processing helix chain 'B' and resid 4876 through 4890 Processing helix chain 'B' and resid 4907 through 4955 Processing helix chain 'B' and resid 4971 through 4979 removed outlier: 3.661A pdb=" N THR B4975 " --> pdb=" O HIS B4971 " (cutoff:3.500A) Processing helix chain 'B' and resid 4983 through 4996 removed outlier: 3.603A pdb=" N MET B4987 " --> pdb=" O LEU B4983 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5014 Processing helix chain 'B' and resid 5025 through 5034 Processing helix chain 'C' and resid 6 through 21 removed outlier: 4.252A pdb=" N ASP C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 65 through 92 removed outlier: 4.569A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.405A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 66 Processing helix chain 'E' and resid 74 through 84 removed outlier: 3.537A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 255 through 258 removed outlier: 4.171A pdb=" N SER E 258 " --> pdb=" O HIS E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 394 through 419 removed outlier: 3.607A pdb=" N SER E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 452 Processing helix chain 'E' and resid 460 through 481 Processing helix chain 'E' and resid 482 through 495 removed outlier: 3.898A pdb=" N LEU E 486 " --> pdb=" O GLY E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 508 Processing helix chain 'E' and resid 511 through 531 removed outlier: 4.202A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG E 531 " --> pdb=" O ALA E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 542 removed outlier: 3.682A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 Processing helix chain 'E' and resid 556 through 571 removed outlier: 3.833A pdb=" N ILE E 560 " --> pdb=" O ALA E 556 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE E 569 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER E 571 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 577 Processing helix chain 'E' and resid 579 through 593 removed outlier: 3.715A pdb=" N ILE E 583 " --> pdb=" O GLN E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 608 removed outlier: 3.964A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E 608 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 625 Processing helix chain 'E' and resid 812 through 815 removed outlier: 3.795A pdb=" N VAL E 815 " --> pdb=" O HIS E 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 812 through 815' Processing helix chain 'E' and resid 864 through 889 Processing helix chain 'E' and resid 914 through 936 Processing helix chain 'E' and resid 943 through 949 Processing helix chain 'E' and resid 955 through 960 removed outlier: 4.004A pdb=" N TYR E 959 " --> pdb=" O LEU E 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET E 960 " --> pdb=" O PRO E 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 955 through 960' Processing helix chain 'E' and resid 978 through 1004 Processing helix chain 'E' and resid 1018 through 1022 removed outlier: 4.216A pdb=" N VAL E1022 " --> pdb=" O PRO E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1050 removed outlier: 3.535A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 1213 through 1222 removed outlier: 3.928A pdb=" N CYS E1217 " --> pdb=" O PHE E1213 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E1219 " --> pdb=" O ALA E1215 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) Processing helix chain 'E' and resid 1444 through 1446 No H-bonds generated for 'chain 'E' and resid 1444 through 1446' Processing helix chain 'E' and resid 1574 through 1580 removed outlier: 3.590A pdb=" N ALA E1578 " --> pdb=" O PRO E1574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E1580 " --> pdb=" O SER E1576 " (cutoff:3.500A) Processing helix chain 'E' and resid 1650 through 1654 Processing helix chain 'E' and resid 1657 through 1674 removed outlier: 4.104A pdb=" N CYS E1674 " --> pdb=" O TYR E1670 " (cutoff:3.500A) Processing helix chain 'E' and resid 1679 through 1689 removed outlier: 3.517A pdb=" N HIS E1683 " --> pdb=" O ASN E1679 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER E1687 " --> pdb=" O HIS E1683 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS E1688 " --> pdb=" O ALA E1684 " (cutoff:3.500A) Processing helix chain 'E' and resid 1690 through 1700 Processing helix chain 'E' and resid 1704 through 1719 removed outlier: 3.575A pdb=" N HIS E1719 " --> pdb=" O LEU E1715 " (cutoff:3.500A) Processing helix chain 'E' and resid 1721 through 1731 Processing helix chain 'E' and resid 1739 through 1744 removed outlier: 3.521A pdb=" N ALA E1744 " --> pdb=" O PRO E1740 " (cutoff:3.500A) Processing helix chain 'E' and resid 1804 through 1826 removed outlier: 3.639A pdb=" N GLN E1825 " --> pdb=" O ARG E1821 " (cutoff:3.500A) Processing helix chain 'E' and resid 1835 through 1853 Proline residue: E1841 - end of helix removed outlier: 3.671A pdb=" N MET E1852 " --> pdb=" O THR E1848 " (cutoff:3.500A) Processing helix chain 'E' and resid 1856 through 1868 removed outlier: 3.591A pdb=" N VAL E1860 " --> pdb=" O GLY E1856 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E1861 " --> pdb=" O ASP E1857 " (cutoff:3.500A) Processing helix chain 'E' and resid 1933 through 1983 removed outlier: 3.690A pdb=" N LYS E1937 " --> pdb=" O PRO E1933 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU E1938 " --> pdb=" O GLU E1934 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN E1939 " --> pdb=" O SER E1935 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E1969 " --> pdb=" O ARG E1965 " (cutoff:3.500A) Processing helix chain 'E' and resid 1988 through 2001 removed outlier: 4.562A pdb=" N GLU E1998 " --> pdb=" O ARG E1994 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE E1999 " --> pdb=" O ARG E1995 " (cutoff:3.500A) Processing helix chain 'E' and resid 2002 through 2011 Processing helix chain 'E' and resid 2028 through 2044 removed outlier: 3.777A pdb=" N LEU E2032 " --> pdb=" O ILE E2028 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY E2044 " --> pdb=" O LEU E2040 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2110 removed outlier: 4.382A pdb=" N ASP E2110 " --> pdb=" O TRP E2106 " (cutoff:3.500A) Processing helix chain 'E' and resid 2114 through 2130 Processing helix chain 'E' and resid 2130 through 2139 removed outlier: 3.564A pdb=" N GLU E2134 " --> pdb=" O ASP E2130 " (cutoff:3.500A) Processing helix chain 'E' and resid 2149 through 2168 removed outlier: 4.017A pdb=" N ILE E2168 " --> pdb=" O ARG E2164 " (cutoff:3.500A) Processing helix chain 'E' and resid 2172 through 2187 Processing helix chain 'E' and resid 2188 through 2189 No H-bonds generated for 'chain 'E' and resid 2188 through 2189' Processing helix chain 'E' and resid 2190 through 2194 Processing helix chain 'E' and resid 2195 through 2203 removed outlier: 4.003A pdb=" N MET E2199 " --> pdb=" O HIS E2195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E2200 " --> pdb=" O PRO E2196 " (cutoff:3.500A) Processing helix chain 'E' and resid 2203 through 2217 Processing helix chain 'E' and resid 2226 through 2242 removed outlier: 3.585A pdb=" N ARG E2242 " --> pdb=" O CYS E2238 " (cutoff:3.500A) Processing helix chain 'E' and resid 2244 through 2253 Processing helix chain 'E' and resid 2254 through 2263 removed outlier: 3.581A pdb=" N LEU E2258 " --> pdb=" O HIS E2254 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY E2263 " --> pdb=" O LEU E2259 " (cutoff:3.500A) Processing helix chain 'E' and resid 2272 through 2282 Processing helix chain 'E' and resid 2284 through 2290 removed outlier: 3.609A pdb=" N ALA E2288 " --> pdb=" O ASN E2284 " (cutoff:3.500A) Processing helix chain 'E' and resid 2292 through 2307 removed outlier: 3.934A pdb=" N LEU E2296 " --> pdb=" O GLN E2292 " (cutoff:3.500A) Processing helix chain 'E' and resid 2311 through 2317 Processing helix chain 'E' and resid 2325 through 2340 removed outlier: 3.851A pdb=" N GLY E2329 " --> pdb=" O ASN E2325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG E2331 " --> pdb=" O CYS E2327 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E2332 " --> pdb=" O GLY E2328 " (cutoff:3.500A) Processing helix chain 'E' and resid 2347 through 2361 removed outlier: 3.892A pdb=" N LYS E2361 " --> pdb=" O LEU E2357 " (cutoff:3.500A) Processing helix chain 'E' and resid 2362 through 2365 Processing helix chain 'E' and resid 2378 through 2385 Processing helix chain 'E' and resid 2421 through 2437 Processing helix chain 'E' and resid 2448 through 2462 removed outlier: 3.685A pdb=" N LEU E2452 " --> pdb=" O LYS E2448 " (cutoff:3.500A) Processing helix chain 'E' and resid 2463 through 2472 removed outlier: 3.763A pdb=" N LEU E2467 " --> pdb=" O PRO E2463 " (cutoff:3.500A) Processing helix chain 'E' and resid 2496 through 2511 removed outlier: 4.209A pdb=" N LYS E2500 " --> pdb=" O VAL E2496 " (cutoff:3.500A) Processing helix chain 'E' and resid 2519 through 2527 Processing helix chain 'E' and resid 2547 through 2566 removed outlier: 3.527A pdb=" N ALA E2558 " --> pdb=" O TYR E2554 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU E2560 " --> pdb=" O CYS E2556 " (cutoff:3.500A) Proline residue: E2561 - end of helix Processing helix chain 'E' and resid 2567 through 2570 Processing helix chain 'E' and resid 2580 through 2592 removed outlier: 3.520A pdb=" N ARG E2592 " --> pdb=" O TYR E2588 " (cutoff:3.500A) Processing helix chain 'E' and resid 2597 through 2613 removed outlier: 3.641A pdb=" N ARG E2613 " --> pdb=" O MET E2609 " (cutoff:3.500A) Processing helix chain 'E' and resid 2616 through 2629 removed outlier: 3.521A pdb=" N LEU E2620 " --> pdb=" O ARG E2616 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E2623 " --> pdb=" O MET E2619 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG E2625 " --> pdb=" O GLN E2621 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG E2626 " --> pdb=" O HIS E2622 " (cutoff:3.500A) Processing helix chain 'E' and resid 2642 through 2653 removed outlier: 4.198A pdb=" N UNK E2646 " --> pdb=" O UNK E2642 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N UNK E2651 " --> pdb=" O UNK E2647 " (cutoff:3.500A) Processing helix chain 'E' and resid 2665 through 2683 removed outlier: 3.513A pdb=" N UNK E2683 " --> pdb=" O UNK E2679 " (cutoff:3.500A) Processing helix chain 'E' and resid 2689 through 2700 Processing helix chain 'E' and resid 2750 through 2772 removed outlier: 4.500A pdb=" N PHE E2754 " --> pdb=" O ALYS E2750 " (cutoff:3.500A) Processing helix chain 'E' and resid 2798 through 2819 removed outlier: 3.676A pdb=" N ILE E2804 " --> pdb=" O LYS E2800 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR E2805 " --> pdb=" O ASP E2801 " (cutoff:3.500A) Proline residue: E2808 - end of helix Processing helix chain 'E' and resid 2868 through 2898 Processing helix chain 'E' and resid 2916 through 2933 removed outlier: 3.778A pdb=" N ASN E2933 " --> pdb=" O PHE E2929 " (cutoff:3.500A) Processing helix chain 'E' and resid 2957 through 2977 Processing helix chain 'E' and resid 3000 through 3018 Processing helix chain 'E' and resid 3033 through 3046 Processing helix chain 'E' and resid 3052 through 3062 Processing helix chain 'E' and resid 3144 through 3163 Processing helix chain 'E' and resid 3174 through 3193 Processing helix chain 'E' and resid 3203 through 3217 Processing helix chain 'E' and resid 3226 through 3238 Processing helix chain 'E' and resid 3279 through 3288 Processing helix chain 'E' and resid 3293 through 3308 Processing helix chain 'E' and resid 3321 through 3335 Processing helix chain 'E' and resid 3347 through 3358 Processing helix chain 'E' and resid 3366 through 3385 Processing helix chain 'E' and resid 3399 through 3427 Proline residue: E3411 - end of helix removed outlier: 6.068A pdb=" N ALA E3422 " --> pdb=" O ASP E3418 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS E3423 " --> pdb=" O ASN E3419 " (cutoff:3.500A) Processing helix chain 'E' and resid 3429 through 3449 Processing helix chain 'E' and resid 3449 through 3461 removed outlier: 3.533A pdb=" N LYS E3453 " --> pdb=" O SER E3449 " (cutoff:3.500A) Processing helix chain 'E' and resid 3510 through 3526 Processing helix chain 'E' and resid 3535 through 3544 Processing helix chain 'E' and resid 3549 through 3555 Processing helix chain 'E' and resid 3566 through 3574 Processing helix chain 'E' and resid 3587 through 3606 Processing helix chain 'E' and resid 3627 through 3632 removed outlier: 3.645A pdb=" N ALA E3630 " --> pdb=" O ALA E3627 " (cutoff:3.500A) Processing helix chain 'E' and resid 3636 through 3640 Processing helix chain 'E' and resid 3641 through 3657 removed outlier: 3.661A pdb=" N GLU E3651 " --> pdb=" O ASN E3647 " (cutoff:3.500A) Processing helix chain 'E' and resid 3665 through 3676 Processing helix chain 'E' and resid 3692 through 3708 removed outlier: 3.525A pdb=" N ALA E3705 " --> pdb=" O PHE E3701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E3706 " --> pdb=" O SER E3702 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E3707 " --> pdb=" O ARG E3703 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E3708 " --> pdb=" O THR E3704 " (cutoff:3.500A) Processing helix chain 'E' and resid 3715 through 3730 removed outlier: 3.602A pdb=" N ASP E3723 " --> pdb=" O MET E3719 " (cutoff:3.500A) Processing helix chain 'E' and resid 3748 through 3767 removed outlier: 4.265A pdb=" N LEU E3765 " --> pdb=" O GLN E3761 " (cutoff:3.500A) Processing helix chain 'E' and resid 3769 through 3782 removed outlier: 4.166A pdb=" N MET E3773 " --> pdb=" O GLY E3769 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E3774 " --> pdb=" O ALA E3770 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU E3775 " --> pdb=" O ALA E3771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE E3778 " --> pdb=" O VAL E3774 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E3782 " --> pdb=" O ILE E3778 " (cutoff:3.500A) Processing helix chain 'E' and resid 3786 through 3797 removed outlier: 3.749A pdb=" N SER E3790 " --> pdb=" O GLY E3786 " (cutoff:3.500A) Processing helix chain 'E' and resid 3805 through 3819 removed outlier: 3.539A pdb=" N TYR E3814 " --> pdb=" O LYS E3810 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E3815 " --> pdb=" O MET E3811 " (cutoff:3.500A) Processing helix chain 'E' and resid 3822 through 3833 Processing helix chain 'E' and resid 3838 through 3850 removed outlier: 4.222A pdb=" N ARG E3844 " --> pdb=" O ASN E3840 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN E3845 " --> pdb=" O ALA E3841 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E3846 " --> pdb=" O PHE E3842 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS E3847 " --> pdb=" O GLU E3843 " (cutoff:3.500A) Processing helix chain 'E' and resid 3872 through 3886 removed outlier: 3.632A pdb=" N THR E3876 " --> pdb=" O ASP E3872 " (cutoff:3.500A) Processing helix chain 'E' and resid 3891 through 3900 removed outlier: 3.854A pdb=" N GLN E3895 " --> pdb=" O ASN E3891 " (cutoff:3.500A) Processing helix chain 'E' and resid 3909 through 3932 removed outlier: 3.579A pdb=" N CYS E3913 " --> pdb=" O ASN E3909 " (cutoff:3.500A) Processing helix chain 'E' and resid 3941 through 3964 Processing helix chain 'E' and resid 3968 through 3977 removed outlier: 3.637A pdb=" N HIS E3977 " --> pdb=" O GLN E3973 " (cutoff:3.500A) Processing helix chain 'E' and resid 3979 through 3999 removed outlier: 3.674A pdb=" N HIS E3989 " --> pdb=" O VAL E3985 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E3990 " --> pdb=" O GLY E3986 " (cutoff:3.500A) Processing helix chain 'E' and resid 4005 through 4026 removed outlier: 3.806A pdb=" N VAL E4020 " --> pdb=" O LYS E4016 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET E4021 " --> pdb=" O ASP E4017 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E4022 " --> pdb=" O MET E4018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E4023 " --> pdb=" O VAL E4019 " (cutoff:3.500A) Processing helix chain 'E' and resid 4033 through 4046 removed outlier: 4.358A pdb=" N ARG E4037 " --> pdb=" O GLY E4033 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E4046 " --> pdb=" O MET E4042 " (cutoff:3.500A) Processing helix chain 'E' and resid 4046 through 4069 removed outlier: 3.503A pdb=" N VAL E4050 " --> pdb=" O SER E4046 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E4063 " --> pdb=" O MET E4059 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS E4064 " --> pdb=" O PHE E4060 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP E4065 " --> pdb=" O LEU E4061 " (cutoff:3.500A) Processing helix chain 'E' and resid 4069 through 4075 removed outlier: 3.880A pdb=" N GLN E4073 " --> pdb=" O SER E4069 " (cutoff:3.500A) Processing helix chain 'E' and resid 4123 through 4127 removed outlier: 3.560A pdb=" N ARG E4126 " --> pdb=" O PHE E4123 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE E4127 " --> pdb=" O ALA E4124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4123 through 4127' Processing helix chain 'E' and resid 4128 through 4148 Processing helix chain 'E' and resid 4152 through 4167 removed outlier: 3.989A pdb=" N LEU E4161 " --> pdb=" O ASN E4157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE E4165 " --> pdb=" O LEU E4161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU E4167 " --> pdb=" O GLU E4163 " (cutoff:3.500A) Processing helix chain 'E' and resid 4168 through 4170 No H-bonds generated for 'chain 'E' and resid 4168 through 4170' Processing helix chain 'E' and resid 4193 through 4201 removed outlier: 3.553A pdb=" N ARG E4197 " --> pdb=" O SER E4193 " (cutoff:3.500A) Processing helix chain 'E' and resid 4202 through 4219 Processing helix chain 'E' and resid 4221 through 4241 removed outlier: 3.530A pdb=" N GLN E4241 " --> pdb=" O ILE E4237 " (cutoff:3.500A) Processing helix chain 'E' and resid 4316 through 4331 Processing helix chain 'E' and resid 4544 through 4576 removed outlier: 5.536A pdb=" N TYR E4558 " --> pdb=" O SER E4554 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR E4559 " --> pdb=" O ARG E4555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE E4562 " --> pdb=" O TYR E4558 " (cutoff:3.500A) Processing helix chain 'E' and resid 4636 through 4682 removed outlier: 3.644A pdb=" N ALA E4640 " --> pdb=" O TYR E4636 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU E4641 " --> pdb=" O MET E4637 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG E4642 " --> pdb=" O GLU E4638 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E4664 " --> pdb=" O ASN E4660 " (cutoff:3.500A) Proline residue: E4665 - end of helix Processing helix chain 'E' and resid 4694 through 4700 removed outlier: 3.681A pdb=" N GLN E4698 " --> pdb=" O ASP E4694 " (cutoff:3.500A) Processing helix chain 'E' and resid 4717 through 4726 Processing helix chain 'E' and resid 4731 through 4737 Processing helix chain 'E' and resid 4762 through 4769 Processing helix chain 'E' and resid 4770 through 4783 removed outlier: 3.657A pdb=" N GLN E4774 " --> pdb=" O ASP E4770 " (cutoff:3.500A) Processing helix chain 'E' and resid 4784 through 4800 Processing helix chain 'E' and resid 4807 through 4815 removed outlier: 4.031A pdb=" N LEU E4811 " --> pdb=" O PHE E4807 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E4812 " --> pdb=" O ALA E4808 " (cutoff:3.500A) Processing helix chain 'E' and resid 4818 through 4827 removed outlier: 3.696A pdb=" N THR E4823 " --> pdb=" O LYS E4819 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E4824 " --> pdb=" O THR E4820 " (cutoff:3.500A) Processing helix chain 'E' and resid 4831 through 4857 removed outlier: 3.886A pdb=" N MET E4837 " --> pdb=" O LYS E4833 " (cutoff:3.500A) Processing helix chain 'E' and resid 4876 through 4890 Processing helix chain 'E' and resid 4907 through 4955 Processing helix chain 'E' and resid 4971 through 4979 removed outlier: 3.661A pdb=" N THR E4975 " --> pdb=" O HIS E4971 " (cutoff:3.500A) Processing helix chain 'E' and resid 4983 through 4996 removed outlier: 3.603A pdb=" N MET E4987 " --> pdb=" O LEU E4983 " (cutoff:3.500A) Processing helix chain 'E' and resid 5002 through 5014 Processing helix chain 'E' and resid 5025 through 5034 Processing helix chain 'F' and resid 6 through 21 removed outlier: 4.252A pdb=" N ASP F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 65 through 92 removed outlier: 4.569A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 38 through 43 removed outlier: 4.405A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'H' and resid 74 through 84 removed outlier: 3.537A pdb=" N ASN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 146 Processing helix chain 'H' and resid 255 through 258 removed outlier: 4.171A pdb=" N SER H 258 " --> pdb=" O HIS H 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 394 through 419 removed outlier: 3.607A pdb=" N SER H 398 " --> pdb=" O GLN H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 452 Processing helix chain 'H' and resid 460 through 481 Processing helix chain 'H' and resid 482 through 495 removed outlier: 3.898A pdb=" N LEU H 486 " --> pdb=" O GLY H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 508 Processing helix chain 'H' and resid 511 through 531 removed outlier: 4.202A pdb=" N LYS H 516 " --> pdb=" O ALA H 512 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU H 517 " --> pdb=" O GLU H 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG H 531 " --> pdb=" O ALA H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 542 removed outlier: 3.682A pdb=" N CYS H 537 " --> pdb=" O ASN H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 549 Processing helix chain 'H' and resid 556 through 571 removed outlier: 3.833A pdb=" N ILE H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE H 569 " --> pdb=" O TYR H 565 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER H 571 " --> pdb=" O VAL H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 577 Processing helix chain 'H' and resid 579 through 593 removed outlier: 3.715A pdb=" N ILE H 583 " --> pdb=" O GLN H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 608 removed outlier: 3.964A pdb=" N LEU H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL H 608 " --> pdb=" O CYS H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 625 Processing helix chain 'H' and resid 812 through 815 removed outlier: 3.795A pdb=" N VAL H 815 " --> pdb=" O HIS H 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 812 through 815' Processing helix chain 'H' and resid 864 through 889 Processing helix chain 'H' and resid 914 through 936 Processing helix chain 'H' and resid 943 through 949 Processing helix chain 'H' and resid 955 through 960 removed outlier: 4.004A pdb=" N TYR H 959 " --> pdb=" O LEU H 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET H 960 " --> pdb=" O PRO H 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 955 through 960' Processing helix chain 'H' and resid 978 through 1004 Processing helix chain 'H' and resid 1018 through 1022 removed outlier: 4.216A pdb=" N VAL H1022 " --> pdb=" O PRO H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1028 through 1050 removed outlier: 3.535A pdb=" N SER H1034 " --> pdb=" O ALA H1030 " (cutoff:3.500A) Processing helix chain 'H' and resid 1213 through 1222 removed outlier: 3.928A pdb=" N CYS H1217 " --> pdb=" O PHE H1213 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H1219 " --> pdb=" O ALA H1215 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN H1220 " --> pdb=" O ILE H1216 " (cutoff:3.500A) Processing helix chain 'H' and resid 1444 through 1446 No H-bonds generated for 'chain 'H' and resid 1444 through 1446' Processing helix chain 'H' and resid 1574 through 1580 removed outlier: 3.590A pdb=" N ALA H1578 " --> pdb=" O PRO H1574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE H1580 " --> pdb=" O SER H1576 " (cutoff:3.500A) Processing helix chain 'H' and resid 1650 through 1654 Processing helix chain 'H' and resid 1657 through 1674 removed outlier: 4.104A pdb=" N CYS H1674 " --> pdb=" O TYR H1670 " (cutoff:3.500A) Processing helix chain 'H' and resid 1679 through 1689 removed outlier: 3.517A pdb=" N HIS H1683 " --> pdb=" O ASN H1679 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H1684 " --> pdb=" O ARG H1680 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER H1687 " --> pdb=" O HIS H1683 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS H1688 " --> pdb=" O ALA H1684 " (cutoff:3.500A) Processing helix chain 'H' and resid 1690 through 1700 Processing helix chain 'H' and resid 1704 through 1719 removed outlier: 3.575A pdb=" N HIS H1719 " --> pdb=" O LEU H1715 " (cutoff:3.500A) Processing helix chain 'H' and resid 1721 through 1731 Processing helix chain 'H' and resid 1739 through 1744 removed outlier: 3.521A pdb=" N ALA H1744 " --> pdb=" O PRO H1740 " (cutoff:3.500A) Processing helix chain 'H' and resid 1804 through 1826 removed outlier: 3.639A pdb=" N GLN H1825 " --> pdb=" O ARG H1821 " (cutoff:3.500A) Processing helix chain 'H' and resid 1835 through 1853 Proline residue: H1841 - end of helix removed outlier: 3.671A pdb=" N MET H1852 " --> pdb=" O THR H1848 " (cutoff:3.500A) Processing helix chain 'H' and resid 1856 through 1868 removed outlier: 3.591A pdb=" N VAL H1860 " --> pdb=" O GLY H1856 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS H1861 " --> pdb=" O ASP H1857 " (cutoff:3.500A) Processing helix chain 'H' and resid 1933 through 1983 removed outlier: 3.690A pdb=" N LYS H1937 " --> pdb=" O PRO H1933 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU H1938 " --> pdb=" O GLU H1934 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN H1939 " --> pdb=" O SER H1935 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS H1969 " --> pdb=" O ARG H1965 " (cutoff:3.500A) Processing helix chain 'H' and resid 1988 through 2001 removed outlier: 4.562A pdb=" N GLU H1998 " --> pdb=" O ARG H1994 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE H1999 " --> pdb=" O ARG H1995 " (cutoff:3.500A) Processing helix chain 'H' and resid 2002 through 2011 Processing helix chain 'H' and resid 2028 through 2044 removed outlier: 3.777A pdb=" N LEU H2032 " --> pdb=" O ILE H2028 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H2044 " --> pdb=" O LEU H2040 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2110 removed outlier: 4.382A pdb=" N ASP H2110 " --> pdb=" O TRP H2106 " (cutoff:3.500A) Processing helix chain 'H' and resid 2114 through 2130 Processing helix chain 'H' and resid 2130 through 2139 removed outlier: 3.564A pdb=" N GLU H2134 " --> pdb=" O ASP H2130 " (cutoff:3.500A) Processing helix chain 'H' and resid 2149 through 2168 removed outlier: 4.017A pdb=" N ILE H2168 " --> pdb=" O ARG H2164 " (cutoff:3.500A) Processing helix chain 'H' and resid 2172 through 2187 Processing helix chain 'H' and resid 2188 through 2189 No H-bonds generated for 'chain 'H' and resid 2188 through 2189' Processing helix chain 'H' and resid 2190 through 2194 Processing helix chain 'H' and resid 2195 through 2203 removed outlier: 4.003A pdb=" N MET H2199 " --> pdb=" O HIS H2195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG H2200 " --> pdb=" O PRO H2196 " (cutoff:3.500A) Processing helix chain 'H' and resid 2203 through 2217 Processing helix chain 'H' and resid 2226 through 2242 removed outlier: 3.585A pdb=" N ARG H2242 " --> pdb=" O CYS H2238 " (cutoff:3.500A) Processing helix chain 'H' and resid 2244 through 2253 Processing helix chain 'H' and resid 2254 through 2263 removed outlier: 3.581A pdb=" N LEU H2258 " --> pdb=" O HIS H2254 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY H2263 " --> pdb=" O LEU H2259 " (cutoff:3.500A) Processing helix chain 'H' and resid 2272 through 2282 Processing helix chain 'H' and resid 2284 through 2290 removed outlier: 3.609A pdb=" N ALA H2288 " --> pdb=" O ASN H2284 " (cutoff:3.500A) Processing helix chain 'H' and resid 2292 through 2307 removed outlier: 3.934A pdb=" N LEU H2296 " --> pdb=" O GLN H2292 " (cutoff:3.500A) Processing helix chain 'H' and resid 2311 through 2317 Processing helix chain 'H' and resid 2325 through 2340 removed outlier: 3.851A pdb=" N GLY H2329 " --> pdb=" O ASN H2325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG H2331 " --> pdb=" O CYS H2327 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR H2332 " --> pdb=" O GLY H2328 " (cutoff:3.500A) Processing helix chain 'H' and resid 2347 through 2361 removed outlier: 3.892A pdb=" N LYS H2361 " --> pdb=" O LEU H2357 " (cutoff:3.500A) Processing helix chain 'H' and resid 2362 through 2365 Processing helix chain 'H' and resid 2378 through 2385 Processing helix chain 'H' and resid 2421 through 2437 Processing helix chain 'H' and resid 2448 through 2462 removed outlier: 3.685A pdb=" N LEU H2452 " --> pdb=" O LYS H2448 " (cutoff:3.500A) Processing helix chain 'H' and resid 2463 through 2472 removed outlier: 3.763A pdb=" N LEU H2467 " --> pdb=" O PRO H2463 " (cutoff:3.500A) Processing helix chain 'H' and resid 2496 through 2511 removed outlier: 4.209A pdb=" N LYS H2500 " --> pdb=" O VAL H2496 " (cutoff:3.500A) Processing helix chain 'H' and resid 2519 through 2527 Processing helix chain 'H' and resid 2547 through 2566 removed outlier: 3.527A pdb=" N ALA H2558 " --> pdb=" O TYR H2554 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU H2560 " --> pdb=" O CYS H2556 " (cutoff:3.500A) Proline residue: H2561 - end of helix Processing helix chain 'H' and resid 2567 through 2570 Processing helix chain 'H' and resid 2580 through 2592 removed outlier: 3.520A pdb=" N ARG H2592 " --> pdb=" O TYR H2588 " (cutoff:3.500A) Processing helix chain 'H' and resid 2597 through 2613 removed outlier: 3.641A pdb=" N ARG H2613 " --> pdb=" O MET H2609 " (cutoff:3.500A) Processing helix chain 'H' and resid 2616 through 2629 removed outlier: 3.521A pdb=" N LEU H2620 " --> pdb=" O ARG H2616 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU H2623 " --> pdb=" O MET H2619 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG H2625 " --> pdb=" O GLN H2621 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG H2626 " --> pdb=" O HIS H2622 " (cutoff:3.500A) Processing helix chain 'H' and resid 2642 through 2653 removed outlier: 4.198A pdb=" N UNK H2646 " --> pdb=" O UNK H2642 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N UNK H2651 " --> pdb=" O UNK H2647 " (cutoff:3.500A) Processing helix chain 'H' and resid 2665 through 2683 removed outlier: 3.513A pdb=" N UNK H2683 " --> pdb=" O UNK H2679 " (cutoff:3.500A) Processing helix chain 'H' and resid 2689 through 2700 Processing helix chain 'H' and resid 2750 through 2772 removed outlier: 4.500A pdb=" N PHE H2754 " --> pdb=" O ALYS H2750 " (cutoff:3.500A) Processing helix chain 'H' and resid 2798 through 2819 removed outlier: 3.676A pdb=" N ILE H2804 " --> pdb=" O LYS H2800 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR H2805 " --> pdb=" O ASP H2801 " (cutoff:3.500A) Proline residue: H2808 - end of helix Processing helix chain 'H' and resid 2868 through 2898 Processing helix chain 'H' and resid 2916 through 2933 removed outlier: 3.778A pdb=" N ASN H2933 " --> pdb=" O PHE H2929 " (cutoff:3.500A) Processing helix chain 'H' and resid 2957 through 2977 Processing helix chain 'H' and resid 3000 through 3018 Processing helix chain 'H' and resid 3033 through 3046 Processing helix chain 'H' and resid 3052 through 3062 Processing helix chain 'H' and resid 3144 through 3163 Processing helix chain 'H' and resid 3174 through 3193 Processing helix chain 'H' and resid 3203 through 3217 Processing helix chain 'H' and resid 3226 through 3238 Processing helix chain 'H' and resid 3279 through 3288 Processing helix chain 'H' and resid 3293 through 3308 Processing helix chain 'H' and resid 3321 through 3335 Processing helix chain 'H' and resid 3347 through 3358 Processing helix chain 'H' and resid 3366 through 3385 Processing helix chain 'H' and resid 3399 through 3427 Proline residue: H3411 - end of helix removed outlier: 6.068A pdb=" N ALA H3422 " --> pdb=" O ASP H3418 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS H3423 " --> pdb=" O ASN H3419 " (cutoff:3.500A) Processing helix chain 'H' and resid 3429 through 3449 Processing helix chain 'H' and resid 3449 through 3461 removed outlier: 3.533A pdb=" N LYS H3453 " --> pdb=" O SER H3449 " (cutoff:3.500A) Processing helix chain 'H' and resid 3510 through 3526 Processing helix chain 'H' and resid 3535 through 3544 Processing helix chain 'H' and resid 3549 through 3555 Processing helix chain 'H' and resid 3566 through 3574 Processing helix chain 'H' and resid 3587 through 3606 Processing helix chain 'H' and resid 3627 through 3632 removed outlier: 3.645A pdb=" N ALA H3630 " --> pdb=" O ALA H3627 " (cutoff:3.500A) Processing helix chain 'H' and resid 3636 through 3640 Processing helix chain 'H' and resid 3641 through 3657 removed outlier: 3.661A pdb=" N GLU H3651 " --> pdb=" O ASN H3647 " (cutoff:3.500A) Processing helix chain 'H' and resid 3665 through 3676 Processing helix chain 'H' and resid 3692 through 3708 removed outlier: 3.525A pdb=" N ALA H3705 " --> pdb=" O PHE H3701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H3706 " --> pdb=" O SER H3702 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H3707 " --> pdb=" O ARG H3703 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H3708 " --> pdb=" O THR H3704 " (cutoff:3.500A) Processing helix chain 'H' and resid 3715 through 3730 removed outlier: 3.602A pdb=" N ASP H3723 " --> pdb=" O MET H3719 " (cutoff:3.500A) Processing helix chain 'H' and resid 3748 through 3767 removed outlier: 4.265A pdb=" N LEU H3765 " --> pdb=" O GLN H3761 " (cutoff:3.500A) Processing helix chain 'H' and resid 3769 through 3782 removed outlier: 4.166A pdb=" N MET H3773 " --> pdb=" O GLY H3769 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL H3774 " --> pdb=" O ALA H3770 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU H3775 " --> pdb=" O ALA H3771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE H3778 " --> pdb=" O VAL H3774 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H3782 " --> pdb=" O ILE H3778 " (cutoff:3.500A) Processing helix chain 'H' and resid 3786 through 3797 removed outlier: 3.749A pdb=" N SER H3790 " --> pdb=" O GLY H3786 " (cutoff:3.500A) Processing helix chain 'H' and resid 3805 through 3819 removed outlier: 3.539A pdb=" N TYR H3814 " --> pdb=" O LYS H3810 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H3815 " --> pdb=" O MET H3811 " (cutoff:3.500A) Processing helix chain 'H' and resid 3822 through 3833 Processing helix chain 'H' and resid 3838 through 3850 removed outlier: 4.222A pdb=" N ARG H3844 " --> pdb=" O ASN H3840 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN H3845 " --> pdb=" O ALA H3841 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN H3846 " --> pdb=" O PHE H3842 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS H3847 " --> pdb=" O GLU H3843 " (cutoff:3.500A) Processing helix chain 'H' and resid 3872 through 3886 removed outlier: 3.632A pdb=" N THR H3876 " --> pdb=" O ASP H3872 " (cutoff:3.500A) Processing helix chain 'H' and resid 3891 through 3900 removed outlier: 3.854A pdb=" N GLN H3895 " --> pdb=" O ASN H3891 " (cutoff:3.500A) Processing helix chain 'H' and resid 3909 through 3932 removed outlier: 3.579A pdb=" N CYS H3913 " --> pdb=" O ASN H3909 " (cutoff:3.500A) Processing helix chain 'H' and resid 3941 through 3964 Processing helix chain 'H' and resid 3968 through 3977 removed outlier: 3.637A pdb=" N HIS H3977 " --> pdb=" O GLN H3973 " (cutoff:3.500A) Processing helix chain 'H' and resid 3979 through 3999 removed outlier: 3.674A pdb=" N HIS H3989 " --> pdb=" O VAL H3985 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL H3990 " --> pdb=" O GLY H3986 " (cutoff:3.500A) Processing helix chain 'H' and resid 4005 through 4026 removed outlier: 3.806A pdb=" N VAL H4020 " --> pdb=" O LYS H4016 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET H4021 " --> pdb=" O ASP H4017 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H4022 " --> pdb=" O MET H4018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H4023 " --> pdb=" O VAL H4019 " (cutoff:3.500A) Processing helix chain 'H' and resid 4033 through 4046 removed outlier: 4.358A pdb=" N ARG H4037 " --> pdb=" O GLY H4033 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER H4046 " --> pdb=" O MET H4042 " (cutoff:3.500A) Processing helix chain 'H' and resid 4046 through 4069 removed outlier: 3.503A pdb=" N VAL H4050 " --> pdb=" O SER H4046 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H4063 " --> pdb=" O MET H4059 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS H4064 " --> pdb=" O PHE H4060 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP H4065 " --> pdb=" O LEU H4061 " (cutoff:3.500A) Processing helix chain 'H' and resid 4069 through 4075 removed outlier: 3.880A pdb=" N GLN H4073 " --> pdb=" O SER H4069 " (cutoff:3.500A) Processing helix chain 'H' and resid 4123 through 4127 removed outlier: 3.560A pdb=" N ARG H4126 " --> pdb=" O PHE H4123 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE H4127 " --> pdb=" O ALA H4124 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4123 through 4127' Processing helix chain 'H' and resid 4128 through 4148 Processing helix chain 'H' and resid 4152 through 4167 removed outlier: 3.989A pdb=" N LEU H4161 " --> pdb=" O ASN H4157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE H4165 " --> pdb=" O LEU H4161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU H4167 " --> pdb=" O GLU H4163 " (cutoff:3.500A) Processing helix chain 'H' and resid 4168 through 4170 No H-bonds generated for 'chain 'H' and resid 4168 through 4170' Processing helix chain 'H' and resid 4193 through 4201 removed outlier: 3.553A pdb=" N ARG H4197 " --> pdb=" O SER H4193 " (cutoff:3.500A) Processing helix chain 'H' and resid 4202 through 4219 Processing helix chain 'H' and resid 4221 through 4241 removed outlier: 3.530A pdb=" N GLN H4241 " --> pdb=" O ILE H4237 " (cutoff:3.500A) Processing helix chain 'H' and resid 4316 through 4331 Processing helix chain 'H' and resid 4544 through 4576 removed outlier: 5.536A pdb=" N TYR H4558 " --> pdb=" O SER H4554 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR H4559 " --> pdb=" O ARG H4555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE H4562 " --> pdb=" O TYR H4558 " (cutoff:3.500A) Processing helix chain 'H' and resid 4636 through 4682 removed outlier: 3.644A pdb=" N ALA H4640 " --> pdb=" O TYR H4636 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H4641 " --> pdb=" O MET H4637 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG H4642 " --> pdb=" O GLU H4638 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H4664 " --> pdb=" O ASN H4660 " (cutoff:3.500A) Proline residue: H4665 - end of helix Processing helix chain 'H' and resid 4694 through 4700 removed outlier: 3.681A pdb=" N GLN H4698 " --> pdb=" O ASP H4694 " (cutoff:3.500A) Processing helix chain 'H' and resid 4717 through 4726 Processing helix chain 'H' and resid 4731 through 4737 Processing helix chain 'H' and resid 4762 through 4769 Processing helix chain 'H' and resid 4770 through 4783 removed outlier: 3.657A pdb=" N GLN H4774 " --> pdb=" O ASP H4770 " (cutoff:3.500A) Processing helix chain 'H' and resid 4784 through 4800 Processing helix chain 'H' and resid 4807 through 4815 removed outlier: 4.031A pdb=" N LEU H4811 " --> pdb=" O PHE H4807 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU H4812 " --> pdb=" O ALA H4808 " (cutoff:3.500A) Processing helix chain 'H' and resid 4818 through 4827 removed outlier: 3.696A pdb=" N THR H4823 " --> pdb=" O LYS H4819 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H4824 " --> pdb=" O THR H4820 " (cutoff:3.500A) Processing helix chain 'H' and resid 4831 through 4857 removed outlier: 3.886A pdb=" N MET H4837 " --> pdb=" O LYS H4833 " (cutoff:3.500A) Processing helix chain 'H' and resid 4876 through 4890 Processing helix chain 'H' and resid 4907 through 4955 Processing helix chain 'H' and resid 4971 through 4979 removed outlier: 3.661A pdb=" N THR H4975 " --> pdb=" O HIS H4971 " (cutoff:3.500A) Processing helix chain 'H' and resid 4983 through 4996 removed outlier: 3.603A pdb=" N MET H4987 " --> pdb=" O LEU H4983 " (cutoff:3.500A) Processing helix chain 'H' and resid 5002 through 5014 Processing helix chain 'H' and resid 5025 through 5034 Processing helix chain 'I' and resid 6 through 21 removed outlier: 4.252A pdb=" N ASP I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 65 through 92 removed outlier: 4.569A pdb=" N ARG I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'J' and resid 38 through 43 removed outlier: 4.405A pdb=" N ARG J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'K' and resid 74 through 84 removed outlier: 3.537A pdb=" N ASN K 84 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 146 Processing helix chain 'K' and resid 255 through 258 removed outlier: 4.171A pdb=" N SER K 258 " --> pdb=" O HIS K 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 255 through 258' Processing helix chain 'K' and resid 394 through 419 removed outlier: 3.607A pdb=" N SER K 398 " --> pdb=" O GLN K 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 452 Processing helix chain 'K' and resid 460 through 481 Processing helix chain 'K' and resid 482 through 495 removed outlier: 3.898A pdb=" N LEU K 486 " --> pdb=" O GLY K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 508 Processing helix chain 'K' and resid 511 through 531 removed outlier: 4.202A pdb=" N LYS K 516 " --> pdb=" O ALA K 512 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU K 517 " --> pdb=" O GLU K 513 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG K 531 " --> pdb=" O ALA K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 533 through 542 removed outlier: 3.682A pdb=" N CYS K 537 " --> pdb=" O ASN K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 544 through 549 Processing helix chain 'K' and resid 556 through 571 removed outlier: 3.833A pdb=" N ILE K 560 " --> pdb=" O ALA K 556 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE K 569 " --> pdb=" O TYR K 565 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER K 571 " --> pdb=" O VAL K 567 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 577 Processing helix chain 'K' and resid 579 through 593 removed outlier: 3.715A pdb=" N ILE K 583 " --> pdb=" O GLN K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 596 through 608 removed outlier: 3.964A pdb=" N LEU K 600 " --> pdb=" O ASN K 596 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL K 608 " --> pdb=" O CYS K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 615 through 625 Processing helix chain 'K' and resid 812 through 815 removed outlier: 3.795A pdb=" N VAL K 815 " --> pdb=" O HIS K 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 812 through 815' Processing helix chain 'K' and resid 864 through 889 Processing helix chain 'K' and resid 914 through 936 Processing helix chain 'K' and resid 943 through 949 Processing helix chain 'K' and resid 955 through 960 removed outlier: 4.004A pdb=" N TYR K 959 " --> pdb=" O LEU K 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET K 960 " --> pdb=" O PRO K 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 955 through 960' Processing helix chain 'K' and resid 978 through 1004 Processing helix chain 'K' and resid 1018 through 1022 removed outlier: 4.216A pdb=" N VAL K1022 " --> pdb=" O PRO K1019 " (cutoff:3.500A) Processing helix chain 'K' and resid 1028 through 1050 removed outlier: 3.535A pdb=" N SER K1034 " --> pdb=" O ALA K1030 " (cutoff:3.500A) Processing helix chain 'K' and resid 1213 through 1222 removed outlier: 3.928A pdb=" N CYS K1217 " --> pdb=" O PHE K1213 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU K1219 " --> pdb=" O ALA K1215 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN K1220 " --> pdb=" O ILE K1216 " (cutoff:3.500A) Processing helix chain 'K' and resid 1444 through 1446 No H-bonds generated for 'chain 'K' and resid 1444 through 1446' Processing helix chain 'K' and resid 1574 through 1580 removed outlier: 3.590A pdb=" N ALA K1578 " --> pdb=" O PRO K1574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE K1580 " --> pdb=" O SER K1576 " (cutoff:3.500A) Processing helix chain 'K' and resid 1650 through 1654 Processing helix chain 'K' and resid 1657 through 1674 removed outlier: 4.104A pdb=" N CYS K1674 " --> pdb=" O TYR K1670 " (cutoff:3.500A) Processing helix chain 'K' and resid 1679 through 1689 removed outlier: 3.517A pdb=" N HIS K1683 " --> pdb=" O ASN K1679 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K1684 " --> pdb=" O ARG K1680 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER K1687 " --> pdb=" O HIS K1683 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS K1688 " --> pdb=" O ALA K1684 " (cutoff:3.500A) Processing helix chain 'K' and resid 1690 through 1700 Processing helix chain 'K' and resid 1704 through 1719 removed outlier: 3.575A pdb=" N HIS K1719 " --> pdb=" O LEU K1715 " (cutoff:3.500A) Processing helix chain 'K' and resid 1721 through 1731 Processing helix chain 'K' and resid 1739 through 1744 removed outlier: 3.521A pdb=" N ALA K1744 " --> pdb=" O PRO K1740 " (cutoff:3.500A) Processing helix chain 'K' and resid 1804 through 1826 removed outlier: 3.639A pdb=" N GLN K1825 " --> pdb=" O ARG K1821 " (cutoff:3.500A) Processing helix chain 'K' and resid 1835 through 1853 Proline residue: K1841 - end of helix removed outlier: 3.671A pdb=" N MET K1852 " --> pdb=" O THR K1848 " (cutoff:3.500A) Processing helix chain 'K' and resid 1856 through 1868 removed outlier: 3.591A pdb=" N VAL K1860 " --> pdb=" O GLY K1856 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS K1861 " --> pdb=" O ASP K1857 " (cutoff:3.500A) Processing helix chain 'K' and resid 1933 through 1983 removed outlier: 3.690A pdb=" N LYS K1937 " --> pdb=" O PRO K1933 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU K1938 " --> pdb=" O GLU K1934 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN K1939 " --> pdb=" O SER K1935 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS K1969 " --> pdb=" O ARG K1965 " (cutoff:3.500A) Processing helix chain 'K' and resid 1988 through 2001 removed outlier: 4.562A pdb=" N GLU K1998 " --> pdb=" O ARG K1994 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE K1999 " --> pdb=" O ARG K1995 " (cutoff:3.500A) Processing helix chain 'K' and resid 2002 through 2011 Processing helix chain 'K' and resid 2028 through 2044 removed outlier: 3.777A pdb=" N LEU K2032 " --> pdb=" O ILE K2028 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY K2044 " --> pdb=" O LEU K2040 " (cutoff:3.500A) Processing helix chain 'K' and resid 2094 through 2110 removed outlier: 4.382A pdb=" N ASP K2110 " --> pdb=" O TRP K2106 " (cutoff:3.500A) Processing helix chain 'K' and resid 2114 through 2130 Processing helix chain 'K' and resid 2130 through 2139 removed outlier: 3.564A pdb=" N GLU K2134 " --> pdb=" O ASP K2130 " (cutoff:3.500A) Processing helix chain 'K' and resid 2149 through 2168 removed outlier: 4.017A pdb=" N ILE K2168 " --> pdb=" O ARG K2164 " (cutoff:3.500A) Processing helix chain 'K' and resid 2172 through 2187 Processing helix chain 'K' and resid 2188 through 2189 No H-bonds generated for 'chain 'K' and resid 2188 through 2189' Processing helix chain 'K' and resid 2190 through 2194 Processing helix chain 'K' and resid 2195 through 2203 removed outlier: 4.003A pdb=" N MET K2199 " --> pdb=" O HIS K2195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG K2200 " --> pdb=" O PRO K2196 " (cutoff:3.500A) Processing helix chain 'K' and resid 2203 through 2217 Processing helix chain 'K' and resid 2226 through 2242 removed outlier: 3.585A pdb=" N ARG K2242 " --> pdb=" O CYS K2238 " (cutoff:3.500A) Processing helix chain 'K' and resid 2244 through 2253 Processing helix chain 'K' and resid 2254 through 2263 removed outlier: 3.581A pdb=" N LEU K2258 " --> pdb=" O HIS K2254 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY K2263 " --> pdb=" O LEU K2259 " (cutoff:3.500A) Processing helix chain 'K' and resid 2272 through 2282 Processing helix chain 'K' and resid 2284 through 2290 removed outlier: 3.609A pdb=" N ALA K2288 " --> pdb=" O ASN K2284 " (cutoff:3.500A) Processing helix chain 'K' and resid 2292 through 2307 removed outlier: 3.934A pdb=" N LEU K2296 " --> pdb=" O GLN K2292 " (cutoff:3.500A) Processing helix chain 'K' and resid 2311 through 2317 Processing helix chain 'K' and resid 2325 through 2340 removed outlier: 3.851A pdb=" N GLY K2329 " --> pdb=" O ASN K2325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG K2331 " --> pdb=" O CYS K2327 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR K2332 " --> pdb=" O GLY K2328 " (cutoff:3.500A) Processing helix chain 'K' and resid 2347 through 2361 removed outlier: 3.892A pdb=" N LYS K2361 " --> pdb=" O LEU K2357 " (cutoff:3.500A) Processing helix chain 'K' and resid 2362 through 2365 Processing helix chain 'K' and resid 2378 through 2385 Processing helix chain 'K' and resid 2421 through 2437 Processing helix chain 'K' and resid 2448 through 2462 removed outlier: 3.685A pdb=" N LEU K2452 " --> pdb=" O LYS K2448 " (cutoff:3.500A) Processing helix chain 'K' and resid 2463 through 2472 removed outlier: 3.763A pdb=" N LEU K2467 " --> pdb=" O PRO K2463 " (cutoff:3.500A) Processing helix chain 'K' and resid 2496 through 2511 removed outlier: 4.209A pdb=" N LYS K2500 " --> pdb=" O VAL K2496 " (cutoff:3.500A) Processing helix chain 'K' and resid 2519 through 2527 Processing helix chain 'K' and resid 2547 through 2566 removed outlier: 3.527A pdb=" N ALA K2558 " --> pdb=" O TYR K2554 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU K2560 " --> pdb=" O CYS K2556 " (cutoff:3.500A) Proline residue: K2561 - end of helix Processing helix chain 'K' and resid 2567 through 2570 Processing helix chain 'K' and resid 2580 through 2592 removed outlier: 3.520A pdb=" N ARG K2592 " --> pdb=" O TYR K2588 " (cutoff:3.500A) Processing helix chain 'K' and resid 2597 through 2613 removed outlier: 3.641A pdb=" N ARG K2613 " --> pdb=" O MET K2609 " (cutoff:3.500A) Processing helix chain 'K' and resid 2616 through 2629 removed outlier: 3.521A pdb=" N LEU K2620 " --> pdb=" O ARG K2616 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU K2623 " --> pdb=" O MET K2619 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG K2625 " --> pdb=" O GLN K2621 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG K2626 " --> pdb=" O HIS K2622 " (cutoff:3.500A) Processing helix chain 'K' and resid 2642 through 2653 removed outlier: 4.198A pdb=" N UNK K2646 " --> pdb=" O UNK K2642 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N UNK K2651 " --> pdb=" O UNK K2647 " (cutoff:3.500A) Processing helix chain 'K' and resid 2665 through 2683 removed outlier: 3.513A pdb=" N UNK K2683 " --> pdb=" O UNK K2679 " (cutoff:3.500A) Processing helix chain 'K' and resid 2689 through 2700 Processing helix chain 'K' and resid 2750 through 2772 removed outlier: 4.500A pdb=" N PHE K2754 " --> pdb=" O ALYS K2750 " (cutoff:3.500A) Processing helix chain 'K' and resid 2798 through 2819 removed outlier: 3.676A pdb=" N ILE K2804 " --> pdb=" O LYS K2800 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR K2805 " --> pdb=" O ASP K2801 " (cutoff:3.500A) Proline residue: K2808 - end of helix Processing helix chain 'K' and resid 2868 through 2898 Processing helix chain 'K' and resid 2916 through 2933 removed outlier: 3.778A pdb=" N ASN K2933 " --> pdb=" O PHE K2929 " (cutoff:3.500A) Processing helix chain 'K' and resid 2957 through 2977 Processing helix chain 'K' and resid 3000 through 3018 Processing helix chain 'K' and resid 3033 through 3046 Processing helix chain 'K' and resid 3052 through 3062 Processing helix chain 'K' and resid 3144 through 3163 Processing helix chain 'K' and resid 3174 through 3193 Processing helix chain 'K' and resid 3203 through 3217 Processing helix chain 'K' and resid 3226 through 3238 Processing helix chain 'K' and resid 3279 through 3288 Processing helix chain 'K' and resid 3293 through 3308 Processing helix chain 'K' and resid 3321 through 3335 Processing helix chain 'K' and resid 3347 through 3358 Processing helix chain 'K' and resid 3366 through 3385 Processing helix chain 'K' and resid 3399 through 3427 Proline residue: K3411 - end of helix removed outlier: 6.068A pdb=" N ALA K3422 " --> pdb=" O ASP K3418 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS K3423 " --> pdb=" O ASN K3419 " (cutoff:3.500A) Processing helix chain 'K' and resid 3429 through 3449 Processing helix chain 'K' and resid 3449 through 3461 removed outlier: 3.533A pdb=" N LYS K3453 " --> pdb=" O SER K3449 " (cutoff:3.500A) Processing helix chain 'K' and resid 3510 through 3526 Processing helix chain 'K' and resid 3535 through 3544 Processing helix chain 'K' and resid 3549 through 3555 Processing helix chain 'K' and resid 3566 through 3574 Processing helix chain 'K' and resid 3587 through 3606 Processing helix chain 'K' and resid 3627 through 3632 removed outlier: 3.645A pdb=" N ALA K3630 " --> pdb=" O ALA K3627 " (cutoff:3.500A) Processing helix chain 'K' and resid 3636 through 3640 Processing helix chain 'K' and resid 3641 through 3657 removed outlier: 3.661A pdb=" N GLU K3651 " --> pdb=" O ASN K3647 " (cutoff:3.500A) Processing helix chain 'K' and resid 3665 through 3676 Processing helix chain 'K' and resid 3692 through 3708 removed outlier: 3.525A pdb=" N ALA K3705 " --> pdb=" O PHE K3701 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU K3706 " --> pdb=" O SER K3702 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR K3707 " --> pdb=" O ARG K3703 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K3708 " --> pdb=" O THR K3704 " (cutoff:3.500A) Processing helix chain 'K' and resid 3715 through 3730 removed outlier: 3.602A pdb=" N ASP K3723 " --> pdb=" O MET K3719 " (cutoff:3.500A) Processing helix chain 'K' and resid 3748 through 3767 removed outlier: 4.265A pdb=" N LEU K3765 " --> pdb=" O GLN K3761 " (cutoff:3.500A) Processing helix chain 'K' and resid 3769 through 3782 removed outlier: 4.166A pdb=" N MET K3773 " --> pdb=" O GLY K3769 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL K3774 " --> pdb=" O ALA K3770 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU K3775 " --> pdb=" O ALA K3771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE K3778 " --> pdb=" O VAL K3774 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS K3782 " --> pdb=" O ILE K3778 " (cutoff:3.500A) Processing helix chain 'K' and resid 3786 through 3797 removed outlier: 3.749A pdb=" N SER K3790 " --> pdb=" O GLY K3786 " (cutoff:3.500A) Processing helix chain 'K' and resid 3805 through 3819 removed outlier: 3.539A pdb=" N TYR K3814 " --> pdb=" O LYS K3810 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K3815 " --> pdb=" O MET K3811 " (cutoff:3.500A) Processing helix chain 'K' and resid 3822 through 3833 Processing helix chain 'K' and resid 3838 through 3850 removed outlier: 4.222A pdb=" N ARG K3844 " --> pdb=" O ASN K3840 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN K3845 " --> pdb=" O ALA K3841 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN K3846 " --> pdb=" O PHE K3842 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS K3847 " --> pdb=" O GLU K3843 " (cutoff:3.500A) Processing helix chain 'K' and resid 3872 through 3886 removed outlier: 3.632A pdb=" N THR K3876 " --> pdb=" O ASP K3872 " (cutoff:3.500A) Processing helix chain 'K' and resid 3891 through 3900 removed outlier: 3.854A pdb=" N GLN K3895 " --> pdb=" O ASN K3891 " (cutoff:3.500A) Processing helix chain 'K' and resid 3909 through 3932 removed outlier: 3.579A pdb=" N CYS K3913 " --> pdb=" O ASN K3909 " (cutoff:3.500A) Processing helix chain 'K' and resid 3941 through 3964 Processing helix chain 'K' and resid 3968 through 3977 removed outlier: 3.637A pdb=" N HIS K3977 " --> pdb=" O GLN K3973 " (cutoff:3.500A) Processing helix chain 'K' and resid 3979 through 3999 removed outlier: 3.674A pdb=" N HIS K3989 " --> pdb=" O VAL K3985 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL K3990 " --> pdb=" O GLY K3986 " (cutoff:3.500A) Processing helix chain 'K' and resid 4005 through 4026 removed outlier: 3.806A pdb=" N VAL K4020 " --> pdb=" O LYS K4016 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET K4021 " --> pdb=" O ASP K4017 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU K4022 " --> pdb=" O MET K4018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU K4023 " --> pdb=" O VAL K4019 " (cutoff:3.500A) Processing helix chain 'K' and resid 4033 through 4046 removed outlier: 4.358A pdb=" N ARG K4037 " --> pdb=" O GLY K4033 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER K4046 " --> pdb=" O MET K4042 " (cutoff:3.500A) Processing helix chain 'K' and resid 4046 through 4069 removed outlier: 3.503A pdb=" N VAL K4050 " --> pdb=" O SER K4046 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K4063 " --> pdb=" O MET K4059 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS K4064 " --> pdb=" O PHE K4060 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K4065 " --> pdb=" O LEU K4061 " (cutoff:3.500A) Processing helix chain 'K' and resid 4069 through 4075 removed outlier: 3.880A pdb=" N GLN K4073 " --> pdb=" O SER K4069 " (cutoff:3.500A) Processing helix chain 'K' and resid 4123 through 4127 removed outlier: 3.560A pdb=" N ARG K4126 " --> pdb=" O PHE K4123 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE K4127 " --> pdb=" O ALA K4124 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 4123 through 4127' Processing helix chain 'K' and resid 4128 through 4148 Processing helix chain 'K' and resid 4152 through 4167 removed outlier: 3.989A pdb=" N LEU K4161 " --> pdb=" O ASN K4157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE K4165 " --> pdb=" O LEU K4161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU K4167 " --> pdb=" O GLU K4163 " (cutoff:3.500A) Processing helix chain 'K' and resid 4168 through 4170 No H-bonds generated for 'chain 'K' and resid 4168 through 4170' Processing helix chain 'K' and resid 4193 through 4201 removed outlier: 3.553A pdb=" N ARG K4197 " --> pdb=" O SER K4193 " (cutoff:3.500A) Processing helix chain 'K' and resid 4202 through 4219 Processing helix chain 'K' and resid 4221 through 4241 removed outlier: 3.530A pdb=" N GLN K4241 " --> pdb=" O ILE K4237 " (cutoff:3.500A) Processing helix chain 'K' and resid 4316 through 4331 Processing helix chain 'K' and resid 4544 through 4576 removed outlier: 5.536A pdb=" N TYR K4558 " --> pdb=" O SER K4554 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR K4559 " --> pdb=" O ARG K4555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE K4562 " --> pdb=" O TYR K4558 " (cutoff:3.500A) Processing helix chain 'K' and resid 4636 through 4682 removed outlier: 3.644A pdb=" N ALA K4640 " --> pdb=" O TYR K4636 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU K4641 " --> pdb=" O MET K4637 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG K4642 " --> pdb=" O GLU K4638 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL K4664 " --> pdb=" O ASN K4660 " (cutoff:3.500A) Proline residue: K4665 - end of helix Processing helix chain 'K' and resid 4694 through 4700 removed outlier: 3.681A pdb=" N GLN K4698 " --> pdb=" O ASP K4694 " (cutoff:3.500A) Processing helix chain 'K' and resid 4717 through 4726 Processing helix chain 'K' and resid 4731 through 4737 Processing helix chain 'K' and resid 4762 through 4769 Processing helix chain 'K' and resid 4770 through 4783 removed outlier: 3.657A pdb=" N GLN K4774 " --> pdb=" O ASP K4770 " (cutoff:3.500A) Processing helix chain 'K' and resid 4784 through 4800 Processing helix chain 'K' and resid 4807 through 4815 removed outlier: 4.031A pdb=" N LEU K4811 " --> pdb=" O PHE K4807 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU K4812 " --> pdb=" O ALA K4808 " (cutoff:3.500A) Processing helix chain 'K' and resid 4818 through 4827 removed outlier: 3.696A pdb=" N THR K4823 " --> pdb=" O LYS K4819 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE K4824 " --> pdb=" O THR K4820 " (cutoff:3.500A) Processing helix chain 'K' and resid 4831 through 4857 removed outlier: 3.886A pdb=" N MET K4837 " --> pdb=" O LYS K4833 " (cutoff:3.500A) Processing helix chain 'K' and resid 4876 through 4890 Processing helix chain 'K' and resid 4907 through 4955 Processing helix chain 'K' and resid 4971 through 4979 removed outlier: 3.661A pdb=" N THR K4975 " --> pdb=" O HIS K4971 " (cutoff:3.500A) Processing helix chain 'K' and resid 4983 through 4996 removed outlier: 3.603A pdb=" N MET K4987 " --> pdb=" O LEU K4983 " (cutoff:3.500A) Processing helix chain 'K' and resid 5002 through 5014 Processing helix chain 'K' and resid 5025 through 5034 Processing helix chain 'L' and resid 6 through 21 removed outlier: 4.252A pdb=" N ASP L 21 " --> pdb=" O PHE L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 65 through 92 removed outlier: 4.569A pdb=" N ARG L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.723A pdb=" N GLU A 3 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.588A pdb=" N ASP A 37 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.189A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.737A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107 removed outlier: 3.928A pdb=" N ILE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.645A pdb=" N SER B 183 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN B 190 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 284 removed outlier: 3.917A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.577A pdb=" N THR B 232 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 246 " --> pdb=" O THR B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.110A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.605A pdb=" N CYS B 315 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 349 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 317 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 347 " --> pdb=" O ARG B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AB4, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.506A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B1638 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AB6, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 664 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 669 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 664 " --> pdb=" O CYS B 746 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 720 through 722 removed outlier: 3.839A pdb=" N GLY B 715 " --> pdb=" O TRP B 722 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 684 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 766 through 769 removed outlier: 3.981A pdb=" N SER B1485 " --> pdb=" O MET B1476 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.653A pdb=" N HIS B1201 " --> pdb=" O GLU B1093 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B1093 " --> pdb=" O HIS B1201 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.914A pdb=" N GLU B1137 " --> pdb=" O ARG B1131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B1124 " --> pdb=" O VAL B1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B1239 " --> pdb=" O ILE B1074 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN B1244 " --> pdb=" O MET B1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B1601 " --> pdb=" O GLN B1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B1287 " --> pdb=" O VAL B1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B1554 " --> pdb=" O LEU B1287 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B1548 " --> pdb=" O VAL B1295 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B1295 " --> pdb=" O LEU B1548 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN B1244 " --> pdb=" O MET B1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B1601 " --> pdb=" O GLN B1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B1287 " --> pdb=" O VAL B1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B1554 " --> pdb=" O LEU B1287 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1255 through 1259 removed outlier: 3.751A pdb=" N GLU B1256 " --> pdb=" O THR B1273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B1273 " --> pdb=" O GLU B1256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B1272 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B1563 " --> pdb=" O ARG B1438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B1438 " --> pdb=" O GLN B1563 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B1565 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B1436 " --> pdb=" O GLU B1565 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B1520 " --> pdb=" O TYR B1433 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET B1527 " --> pdb=" O THR B1538 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR B1538 " --> pdb=" O MET B1527 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B1529 " --> pdb=" O SER B1536 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B1534 " --> pdb=" O ALA B1531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1734 through 1737 removed outlier: 6.365A pdb=" N TYR B1734 " --> pdb=" O TYR B2143 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B2145 " --> pdb=" O TYR B1734 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B1736 " --> pdb=" O ILE B2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 2341 through 2342 removed outlier: 4.117A pdb=" N VAL B2342 " --> pdb=" O GLU B2345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 2776 through 2777 removed outlier: 6.951A pdb=" N SER B2776 " --> pdb=" O HIS B2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 2822 through 2825 removed outlier: 3.741A pdb=" N GLU B2824 " --> pdb=" O ALA B2936 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.723A pdb=" N GLU D 3 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 28 through 29 removed outlier: 3.588A pdb=" N ASP D 37 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 47 through 52 removed outlier: 3.511A pdb=" N LYS E 34 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU E 33 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 26 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU E 22 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 10.737A pdb=" N ALA E 39 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N VAL E 20 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU E 19 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AD5, first strand: chain 'E' and resid 106 through 107 removed outlier: 3.928A pdb=" N ILE E 170 " --> pdb=" O HIS E 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 117 through 120 Processing sheet with id=AD7, first strand: chain 'E' and resid 179 through 183 removed outlier: 3.645A pdb=" N SER E 183 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN E 190 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 284 removed outlier: 3.917A pdb=" N THR E 391 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 232 through 233 removed outlier: 3.577A pdb=" N THR E 232 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR E 246 " --> pdb=" O THR E 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 290 through 292 removed outlier: 4.110A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 315 through 317 removed outlier: 3.605A pdb=" N CYS E 315 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 349 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 317 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 347 " --> pdb=" O ARG E 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 356 through 359 Processing sheet with id=AE4, first strand: chain 'E' and resid 634 through 639 removed outlier: 3.506A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E1638 " --> pdb=" O ASN E 636 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 644 through 645 Processing sheet with id=AE6, first strand: chain 'E' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE E 664 " --> pdb=" O CYS E 746 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP E 669 " --> pdb=" O LYS E 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS E 788 " --> pdb=" O ASP E 669 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP E 742 " --> pdb=" O VAL E 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE E 664 " --> pdb=" O CYS E 746 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 720 through 722 removed outlier: 3.839A pdb=" N GLY E 715 " --> pdb=" O TRP E 722 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL E 684 " --> pdb=" O PHE E 716 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 766 through 769 removed outlier: 3.981A pdb=" N SER E1485 " --> pdb=" O MET E1476 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 830 through 831 removed outlier: 3.653A pdb=" N HIS E1201 " --> pdb=" O GLU E1093 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E1093 " --> pdb=" O HIS E1201 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 1136 through 1138 removed outlier: 3.914A pdb=" N GLU E1137 " --> pdb=" O ARG E1131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E1124 " --> pdb=" O VAL E1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA E1077 " --> pdb=" O PRO E1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E1073 " --> pdb=" O LEU E1194 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E1239 " --> pdb=" O ILE E1074 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN E1244 " --> pdb=" O MET E1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E1601 " --> pdb=" O GLN E1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE E1288 " --> pdb=" O LEU E1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E1287 " --> pdb=" O VAL E1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL E1554 " --> pdb=" O LEU E1287 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU E1548 " --> pdb=" O VAL E1295 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E1295 " --> pdb=" O LEU E1548 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN E1244 " --> pdb=" O MET E1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E1601 " --> pdb=" O GLN E1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE E1288 " --> pdb=" O LEU E1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E1287 " --> pdb=" O VAL E1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL E1554 " --> pdb=" O LEU E1287 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 1255 through 1259 removed outlier: 3.751A pdb=" N GLU E1256 " --> pdb=" O THR E1273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR E1273 " --> pdb=" O GLU E1256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E1272 " --> pdb=" O ILE E1562 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE E1562 " --> pdb=" O LEU E1272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E1563 " --> pdb=" O ARG E1438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E1438 " --> pdb=" O GLN E1563 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E1565 " --> pdb=" O SER E1436 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E1436 " --> pdb=" O GLU E1565 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E1520 " --> pdb=" O TYR E1433 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET E1527 " --> pdb=" O THR E1538 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR E1538 " --> pdb=" O MET E1527 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE E1529 " --> pdb=" O SER E1536 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E1534 " --> pdb=" O ALA E1531 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1734 through 1737 removed outlier: 6.365A pdb=" N TYR E1734 " --> pdb=" O TYR E2143 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE E2145 " --> pdb=" O TYR E1734 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL E1736 " --> pdb=" O ILE E2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 2341 through 2342 removed outlier: 4.117A pdb=" N VAL E2342 " --> pdb=" O GLU E2345 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 2776 through 2777 removed outlier: 6.951A pdb=" N SER E2776 " --> pdb=" O HIS E2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 2822 through 2825 removed outlier: 3.741A pdb=" N GLU E2824 " --> pdb=" O ALA E2936 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.723A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 28 through 29 removed outlier: 3.588A pdb=" N ASP G 37 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 47 through 51 removed outlier: 4.189A pdb=" N LEU H 33 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 26 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU H 22 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 10.737A pdb=" N ALA H 39 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N VAL H 20 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU H 19 " --> pdb=" O ILE H 205 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 67 through 69 Processing sheet with id=AG5, first strand: chain 'H' and resid 106 through 107 removed outlier: 3.928A pdb=" N ILE H 170 " --> pdb=" O HIS H 151 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 117 through 120 Processing sheet with id=AG7, first strand: chain 'H' and resid 179 through 183 removed outlier: 3.645A pdb=" N SER H 183 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN H 190 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 281 through 284 removed outlier: 3.917A pdb=" N THR H 391 " --> pdb=" O ARG H 221 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 232 through 233 removed outlier: 3.577A pdb=" N THR H 232 " --> pdb=" O TYR H 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR H 246 " --> pdb=" O THR H 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'H' and resid 290 through 292 removed outlier: 4.110A pdb=" N VAL H 300 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 315 through 317 removed outlier: 3.605A pdb=" N CYS H 315 " --> pdb=" O GLN H 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 349 " --> pdb=" O CYS H 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG H 317 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H 347 " --> pdb=" O ARG H 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'H' and resid 356 through 359 Processing sheet with id=AH4, first strand: chain 'H' and resid 634 through 639 removed outlier: 3.506A pdb=" N GLN H 634 " --> pdb=" O HIS H1640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H1638 " --> pdb=" O ASN H 636 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 644 through 645 Processing sheet with id=AH6, first strand: chain 'H' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP H 742 " --> pdb=" O VAL H 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE H 664 " --> pdb=" O CYS H 746 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP H 669 " --> pdb=" O LYS H 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS H 788 " --> pdb=" O ASP H 669 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP H 742 " --> pdb=" O VAL H 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE H 664 " --> pdb=" O CYS H 746 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 720 through 722 removed outlier: 3.839A pdb=" N GLY H 715 " --> pdb=" O TRP H 722 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL H 684 " --> pdb=" O PHE H 716 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 766 through 769 removed outlier: 3.981A pdb=" N SER H1485 " --> pdb=" O MET H1476 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 830 through 831 removed outlier: 3.653A pdb=" N HIS H1201 " --> pdb=" O GLU H1093 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU H1093 " --> pdb=" O HIS H1201 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 1136 through 1138 removed outlier: 3.914A pdb=" N GLU H1137 " --> pdb=" O ARG H1131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H1124 " --> pdb=" O VAL H1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H1077 " --> pdb=" O PRO H1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG H1073 " --> pdb=" O LEU H1194 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE H1074 " --> pdb=" O SER H1239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER H1239 " --> pdb=" O ILE H1074 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN H1244 " --> pdb=" O MET H1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET H1601 " --> pdb=" O GLN H1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE H1288 " --> pdb=" O LEU H1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU H1287 " --> pdb=" O VAL H1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL H1554 " --> pdb=" O LEU H1287 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU H1548 " --> pdb=" O VAL H1295 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H1295 " --> pdb=" O LEU H1548 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN H1244 " --> pdb=" O MET H1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET H1601 " --> pdb=" O GLN H1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE H1288 " --> pdb=" O LEU H1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU H1287 " --> pdb=" O VAL H1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL H1554 " --> pdb=" O LEU H1287 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 1255 through 1259 removed outlier: 3.751A pdb=" N GLU H1256 " --> pdb=" O THR H1273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H1273 " --> pdb=" O GLU H1256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H1272 " --> pdb=" O ILE H1562 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE H1562 " --> pdb=" O LEU H1272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H1563 " --> pdb=" O ARG H1438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG H1438 " --> pdb=" O GLN H1563 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU H1565 " --> pdb=" O SER H1436 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER H1436 " --> pdb=" O GLU H1565 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H1520 " --> pdb=" O TYR H1433 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET H1527 " --> pdb=" O THR H1538 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR H1538 " --> pdb=" O MET H1527 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE H1529 " --> pdb=" O SER H1536 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS H1534 " --> pdb=" O ALA H1531 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 1734 through 1737 removed outlier: 6.365A pdb=" N TYR H1734 " --> pdb=" O TYR H2143 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE H2145 " --> pdb=" O TYR H1734 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL H1736 " --> pdb=" O ILE H2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'H' and resid 2341 through 2342 removed outlier: 4.117A pdb=" N VAL H2342 " --> pdb=" O GLU H2345 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 2776 through 2777 removed outlier: 6.951A pdb=" N SER H2776 " --> pdb=" O HIS H2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'H' and resid 2822 through 2825 removed outlier: 3.741A pdb=" N GLU H2824 " --> pdb=" O ALA H2936 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.723A pdb=" N GLU J 3 " --> pdb=" O THR J 75 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.588A pdb=" N ASP J 37 " --> pdb=" O GLY J 28 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 47 through 51 removed outlier: 4.189A pdb=" N LEU K 33 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA K 26 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU K 22 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 10.737A pdb=" N ALA K 39 " --> pdb=" O VAL K 20 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N VAL K 20 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU K 19 " --> pdb=" O ILE K 205 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AJ5, first strand: chain 'K' and resid 106 through 107 removed outlier: 3.928A pdb=" N ILE K 170 " --> pdb=" O HIS K 151 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 117 through 120 Processing sheet with id=AJ7, first strand: chain 'K' and resid 179 through 183 removed outlier: 3.645A pdb=" N SER K 183 " --> pdb=" O GLN K 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN K 190 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 281 through 284 removed outlier: 3.917A pdb=" N THR K 391 " --> pdb=" O ARG K 221 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'K' and resid 232 through 233 removed outlier: 3.577A pdb=" N THR K 232 " --> pdb=" O TYR K 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR K 246 " --> pdb=" O THR K 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'K' and resid 290 through 292 removed outlier: 4.110A pdb=" N VAL K 300 " --> pdb=" O ALA K 292 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 315 through 317 removed outlier: 3.605A pdb=" N CYS K 315 " --> pdb=" O GLN K 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K 349 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG K 317 " --> pdb=" O PHE K 347 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE K 347 " --> pdb=" O ARG K 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'K' and resid 356 through 359 Processing sheet with id=AK4, first strand: chain 'K' and resid 634 through 639 removed outlier: 3.506A pdb=" N GLN K 634 " --> pdb=" O HIS K1640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K1638 " --> pdb=" O ASN K 636 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'K' and resid 644 through 645 Processing sheet with id=AK6, first strand: chain 'K' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP K 742 " --> pdb=" O VAL K 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE K 664 " --> pdb=" O CYS K 746 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP K 669 " --> pdb=" O LYS K 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS K 788 " --> pdb=" O ASP K 669 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'K' and resid 762 through 763 removed outlier: 3.902A pdb=" N ASP K 742 " --> pdb=" O VAL K 668 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE K 664 " --> pdb=" O CYS K 746 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 720 through 722 removed outlier: 3.839A pdb=" N GLY K 715 " --> pdb=" O TRP K 722 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL K 684 " --> pdb=" O PHE K 716 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 766 through 769 removed outlier: 3.981A pdb=" N SER K1485 " --> pdb=" O MET K1476 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 830 through 831 removed outlier: 3.653A pdb=" N HIS K1201 " --> pdb=" O GLU K1093 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K1093 " --> pdb=" O HIS K1201 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 1136 through 1138 removed outlier: 3.914A pdb=" N GLU K1137 " --> pdb=" O ARG K1131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE K1124 " --> pdb=" O VAL K1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA K1077 " --> pdb=" O PRO K1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG K1073 " --> pdb=" O LEU K1194 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE K1074 " --> pdb=" O SER K1239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER K1239 " --> pdb=" O ILE K1074 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN K1244 " --> pdb=" O MET K1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET K1601 " --> pdb=" O GLN K1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE K1288 " --> pdb=" O LEU K1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU K1287 " --> pdb=" O VAL K1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL K1554 " --> pdb=" O LEU K1287 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU K1548 " --> pdb=" O VAL K1295 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K1295 " --> pdb=" O LEU K1548 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N GLN K1244 " --> pdb=" O MET K1601 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET K1601 " --> pdb=" O GLN K1244 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE K1288 " --> pdb=" O LEU K1600 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU K1287 " --> pdb=" O VAL K1554 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL K1554 " --> pdb=" O LEU K1287 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 1255 through 1259 removed outlier: 3.751A pdb=" N GLU K1256 " --> pdb=" O THR K1273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR K1273 " --> pdb=" O GLU K1256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU K1272 " --> pdb=" O ILE K1562 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE K1562 " --> pdb=" O LEU K1272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN K1563 " --> pdb=" O ARG K1438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG K1438 " --> pdb=" O GLN K1563 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU K1565 " --> pdb=" O SER K1436 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER K1436 " --> pdb=" O GLU K1565 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL K1520 " --> pdb=" O TYR K1433 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET K1527 " --> pdb=" O THR K1538 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR K1538 " --> pdb=" O MET K1527 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE K1529 " --> pdb=" O SER K1536 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS K1534 " --> pdb=" O ALA K1531 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 1734 through 1737 removed outlier: 6.365A pdb=" N TYR K1734 " --> pdb=" O TYR K2143 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE K2145 " --> pdb=" O TYR K1734 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL K1736 " --> pdb=" O ILE K2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'K' and resid 2341 through 2342 removed outlier: 4.117A pdb=" N VAL K2342 " --> pdb=" O GLU K2345 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 2776 through 2777 removed outlier: 6.951A pdb=" N SER K2776 " --> pdb=" O HIS K2788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'K' and resid 2822 through 2825 removed outlier: 3.741A pdb=" N GLU K2824 " --> pdb=" O ALA K2936 " (cutoff:3.500A) 6753 hydrogen bonds defined for protein. 19767 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: 82.86 Time building geometry restraints manager: 35.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 37273 1.34 - 1.46: 20636 1.46 - 1.58: 55007 1.58 - 1.69: 0 1.69 - 1.81: 1056 Bond restraints: 113972 Sorted by residual: bond pdb=" CA PRO B 59 " pdb=" C PRO B 59 " ideal model delta sigma weight residual 1.517 1.558 -0.041 9.30e-03 1.16e+04 1.94e+01 bond pdb=" C VAL K 58 " pdb=" N PRO K 59 " ideal model delta sigma weight residual 1.329 1.367 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" C PRO B 59 " pdb=" N PRO B 60 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.90e+00 bond pdb=" CA VAL K 58 " pdb=" C VAL K 58 " ideal model delta sigma weight residual 1.524 1.549 -0.024 1.05e-02 9.07e+03 5.26e+00 bond pdb=" CA VAL K 58 " pdb=" CB VAL K 58 " ideal model delta sigma weight residual 1.537 1.556 -0.019 1.29e-02 6.01e+03 2.15e+00 ... (remaining 113967 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.92: 3247 106.92 - 113.68: 63394 113.68 - 120.45: 42619 120.45 - 127.21: 45183 127.21 - 133.97: 1165 Bond angle restraints: 155608 Sorted by residual: angle pdb=" N ASN E 54 " pdb=" CA ASN E 54 " pdb=" C ASN E 54 " ideal model delta sigma weight residual 112.59 103.19 9.40 1.22e+00 6.72e-01 5.93e+01 angle pdb=" N SER H 53 " pdb=" CA SER H 53 " pdb=" C SER H 53 " ideal model delta sigma weight residual 111.28 118.36 -7.08 1.09e+00 8.42e-01 4.22e+01 angle pdb=" N THR H 52 " pdb=" CA THR H 52 " pdb=" C THR H 52 " ideal model delta sigma weight residual 111.36 117.19 -5.83 1.09e+00 8.42e-01 2.86e+01 angle pdb=" C VAL K 58 " pdb=" N PRO K 59 " pdb=" CA PRO K 59 " ideal model delta sigma weight residual 120.38 115.66 4.72 1.03e+00 9.43e-01 2.10e+01 angle pdb=" C VAL H 58 " pdb=" N PRO H 59 " pdb=" CA PRO H 59 " ideal model delta sigma weight residual 120.38 116.35 4.03 1.03e+00 9.43e-01 1.53e+01 ... (remaining 155603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 64995 17.36 - 34.72: 1585 34.72 - 52.08: 415 52.08 - 69.44: 5 69.44 - 86.80: 8 Dihedral angle restraints: 67008 sinusoidal: 20100 harmonic: 46908 Sorted by residual: dihedral pdb=" N SER H 53 " pdb=" CA SER H 53 " pdb=" CB SER H 53 " pdb=" OG SER H 53 " ideal model delta sinusoidal sigma weight residual -60.00 -115.40 55.40 3 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CA LYS E4209 " pdb=" CB LYS E4209 " pdb=" CG LYS E4209 " pdb=" CD LYS E4209 " ideal model delta sinusoidal sigma weight residual -60.00 -111.12 51.12 3 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CA LYS H4209 " pdb=" CB LYS H4209 " pdb=" CG LYS H4209 " pdb=" CD LYS H4209 " ideal model delta sinusoidal sigma weight residual -60.00 -111.12 51.12 3 1.50e+01 4.44e-03 8.98e+00 ... (remaining 67005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 17307 0.061 - 0.122: 1452 0.122 - 0.184: 13 0.184 - 0.245: 2 0.245 - 0.306: 2 Chirality restraints: 18776 Sorted by residual: chirality pdb=" CA VAL H 58 " pdb=" N VAL H 58 " pdb=" C VAL H 58 " pdb=" CB VAL H 58 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA SER H 53 " pdb=" N SER H 53 " pdb=" C SER H 53 " pdb=" CB SER H 53 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 18773 not shown) Planarity restraints: 20052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 50 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO H 51 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO H 51 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 51 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 50 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO K 51 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 51 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 51 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 50 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO B 51 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.037 5.00e-02 4.00e+02 ... (remaining 20049 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7685 2.74 - 3.28: 109089 3.28 - 3.82: 183755 3.82 - 4.36: 181843 4.36 - 4.90: 333901 Nonbonded interactions: 816273 Sorted by model distance: nonbonded pdb=" O TRP B 686 " pdb=" OG SER B 713 " model vdw 2.202 2.440 nonbonded pdb=" O TRP E 686 " pdb=" OG SER E 713 " model vdw 2.202 2.440 nonbonded pdb=" O TRP H 686 " pdb=" OG SER H 713 " model vdw 2.202 2.440 nonbonded pdb=" O TRP K 686 " pdb=" OG SER K 713 " model vdw 2.202 2.440 nonbonded pdb=" O PHE K2122 " pdb=" OH TYR K3721 " model vdw 2.255 2.440 ... (remaining 816268 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 12 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 5034 or resid 5101)) selection = (chain 'E' and (resid 12 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 5034 or resid 5101)) selection = (chain 'H' and (resid 12 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 5034 or resid 5101)) selection = (chain 'K' and (resid 12 through 2745 or resid 2747 through 2749 or resid 2751 t \ hrough 2761 or resid 2763 through 2806 or resid 2808 through 2869 or resid 2871 \ through 2924 or resid 2926 through 5034 or resid 5101)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.520 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: 0.070 Extract box with map and model: 24.810 Check model and map are aligned: 1.290 Set scattering table: 0.830 Process input model: 339.470 Find NCS groups from input model: 6.070 Set up NCS constraints: 0.800 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:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 379.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 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 : 0.001 0.041 113972 Z= 0.090 Angle : 0.373 9.397 155608 Z= 0.213 Chirality : 0.033 0.306 18776 Planarity : 0.003 0.067 20052 Dihedral : 8.422 86.803 36472 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.84 % Favored : 98.14 % Rotamer: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.06), residues: 14452 helix: 0.48 (0.06), residues: 7228 sheet: -1.54 (0.14), residues: 1160 loop : -2.09 (0.07), residues: 6064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E2324 HIS 0.002 0.000 HIS K 105 PHE 0.013 0.001 PHE E4056 TYR 0.008 0.000 TYR K3721 ARG 0.002 0.000 ARG K 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3144 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3139 time to evaluate : 8.663 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: A 102 GLU cc_start: 0.8463 (tt0) cc_final: 0.7934 (tp30) REVERT: B 15 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6864 (mtt180) REVERT: B 25 ASN cc_start: 0.7923 (m-40) cc_final: 0.7716 (m-40) REVERT: B 53 SER cc_start: 0.6582 (OUTLIER) cc_final: 0.6297 (p) REVERT: B 130 LYS cc_start: 0.8843 (tptp) cc_final: 0.8173 (pttt) REVERT: B 148 TRP cc_start: 0.8903 (m100) cc_final: 0.8610 (m100) REVERT: B 175 SER cc_start: 0.8774 (p) cc_final: 0.8272 (t) REVERT: B 336 PRO cc_start: 0.7004 (Cg_exo) cc_final: 0.6793 (Cg_endo) REVERT: B 467 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8110 (mmmt) REVERT: B 573 GLU cc_start: 0.8472 (mp0) cc_final: 0.7734 (mt-10) REVERT: B 622 THR cc_start: 0.8941 (m) cc_final: 0.8707 (p) REVERT: B 667 MET cc_start: 0.6090 (ttt) cc_final: 0.5879 (tmm) REVERT: B 1100 MET cc_start: 0.8215 (ptp) cc_final: 0.7624 (ptt) REVERT: B 1245 PHE cc_start: 0.8593 (m-80) cc_final: 0.7964 (m-80) REVERT: B 1444 GLU cc_start: 0.7222 (mp0) cc_final: 0.6975 (mp0) REVERT: B 1748 PHE cc_start: 0.8378 (m-80) cc_final: 0.7903 (m-80) REVERT: B 1970 LEU cc_start: 0.7838 (tp) cc_final: 0.7545 (mt) REVERT: B 2013 PHE cc_start: 0.7525 (t80) cc_final: 0.7064 (t80) REVERT: B 2193 TYR cc_start: 0.7551 (m-80) cc_final: 0.7262 (m-80) REVERT: B 2239 TYR cc_start: 0.7643 (m-80) cc_final: 0.7322 (m-80) REVERT: B 2261 ASN cc_start: 0.8971 (m110) cc_final: 0.8700 (m110) REVERT: B 2275 ASP cc_start: 0.7840 (t0) cc_final: 0.7598 (t0) REVERT: B 2349 GLU cc_start: 0.6171 (mp0) cc_final: 0.5868 (mp0) REVERT: B 2547 MET cc_start: 0.7336 (tpp) cc_final: 0.6759 (tpt) REVERT: B 2616 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.5981 (mtt180) REVERT: B 3634 MET cc_start: 0.7903 (mmp) cc_final: 0.7682 (mmm) REVERT: B 3719 MET cc_start: 0.7716 (ttm) cc_final: 0.7424 (tpp) REVERT: B 3727 LYS cc_start: 0.8490 (mttm) cc_final: 0.8086 (mmtm) REVERT: B 3789 VAL cc_start: 0.8719 (t) cc_final: 0.8492 (t) REVERT: B 3806 ASP cc_start: 0.6338 (p0) cc_final: 0.5136 (m-30) REVERT: B 3870 MET cc_start: 0.8209 (mtp) cc_final: 0.7906 (mtp) REVERT: B 3900 THR cc_start: 0.8409 (t) cc_final: 0.8175 (m) REVERT: B 4029 ASN cc_start: 0.7407 (t0) cc_final: 0.7090 (t0) REVERT: B 4034 MET cc_start: 0.5073 (mtt) cc_final: 0.4471 (mmt) REVERT: B 4059 MET cc_start: 0.5870 (mtt) cc_final: 0.5561 (mtp) REVERT: B 4187 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6672 (mtt-85) REVERT: B 4668 ILE cc_start: 0.8541 (mm) cc_final: 0.8300 (tp) REVERT: B 4670 LYS cc_start: 0.5203 (ttmt) cc_final: 0.4882 (mmmt) REVERT: B 4796 MET cc_start: 0.8206 (mmt) cc_final: 0.7755 (mmt) REVERT: B 4798 LEU cc_start: 0.8682 (mt) cc_final: 0.8461 (mt) REVERT: B 5011 MET cc_start: 0.7505 (mmt) cc_final: 0.7138 (tpp) REVERT: B 5018 ASP cc_start: 0.7487 (t0) cc_final: 0.7070 (t0) REVERT: C 93 PHE cc_start: 0.6860 (t80) cc_final: 0.6651 (t80) REVERT: D 102 GLU cc_start: 0.8458 (tt0) cc_final: 0.7934 (tp30) REVERT: E 15 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6865 (mtt180) REVERT: E 25 ASN cc_start: 0.7929 (m-40) cc_final: 0.7728 (m-40) REVERT: E 130 LYS cc_start: 0.8837 (tptp) cc_final: 0.8173 (pttt) REVERT: E 148 TRP cc_start: 0.8906 (m100) cc_final: 0.8611 (m100) REVERT: E 175 SER cc_start: 0.8765 (p) cc_final: 0.8259 (t) REVERT: E 282 ILE cc_start: 0.5898 (mm) cc_final: 0.5658 (mm) REVERT: E 336 PRO cc_start: 0.7016 (Cg_exo) cc_final: 0.6802 (Cg_endo) REVERT: E 467 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8104 (mmmt) REVERT: E 524 GLU cc_start: 0.7865 (tp30) cc_final: 0.7409 (tp30) REVERT: E 573 GLU cc_start: 0.8471 (mp0) cc_final: 0.7761 (mt-10) REVERT: E 622 THR cc_start: 0.8941 (m) cc_final: 0.8716 (p) REVERT: E 667 MET cc_start: 0.6078 (ttt) cc_final: 0.5873 (tmm) REVERT: E 1100 MET cc_start: 0.8212 (ptp) cc_final: 0.7623 (ptt) REVERT: E 1245 PHE cc_start: 0.8591 (m-80) cc_final: 0.7971 (m-80) REVERT: E 1444 GLU cc_start: 0.7222 (mp0) cc_final: 0.6967 (mp0) REVERT: E 1748 PHE cc_start: 0.8372 (m-80) cc_final: 0.7903 (m-80) REVERT: E 1970 LEU cc_start: 0.7840 (tp) cc_final: 0.7542 (mt) REVERT: E 2013 PHE cc_start: 0.7517 (t80) cc_final: 0.7057 (t80) REVERT: E 2193 TYR cc_start: 0.7547 (m-80) cc_final: 0.7256 (m-80) REVERT: E 2239 TYR cc_start: 0.7640 (m-80) cc_final: 0.7329 (m-80) REVERT: E 2261 ASN cc_start: 0.8972 (m110) cc_final: 0.8699 (m110) REVERT: E 2275 ASP cc_start: 0.7843 (t0) cc_final: 0.7602 (t0) REVERT: E 2547 MET cc_start: 0.7336 (tpp) cc_final: 0.6763 (tpt) REVERT: E 2616 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.5978 (mtt180) REVERT: E 3634 MET cc_start: 0.7911 (mmp) cc_final: 0.7694 (mmm) REVERT: E 3719 MET cc_start: 0.7719 (ttm) cc_final: 0.7413 (tpp) REVERT: E 3727 LYS cc_start: 0.8497 (mttm) cc_final: 0.8084 (mmtm) REVERT: E 3789 VAL cc_start: 0.8722 (t) cc_final: 0.8479 (t) REVERT: E 3806 ASP cc_start: 0.6347 (p0) cc_final: 0.5114 (m-30) REVERT: E 3870 MET cc_start: 0.8215 (mtp) cc_final: 0.7900 (mtp) REVERT: E 3900 THR cc_start: 0.8418 (t) cc_final: 0.8197 (m) REVERT: E 4029 ASN cc_start: 0.7399 (t0) cc_final: 0.7098 (t0) REVERT: E 4034 MET cc_start: 0.5092 (mtt) cc_final: 0.4479 (mmt) REVERT: E 4059 MET cc_start: 0.5867 (mtt) cc_final: 0.5647 (mtt) REVERT: E 4187 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6671 (mtt-85) REVERT: E 4668 ILE cc_start: 0.8542 (mm) cc_final: 0.8302 (tp) REVERT: E 4670 LYS cc_start: 0.5194 (ttmt) cc_final: 0.4882 (mmmt) REVERT: E 4796 MET cc_start: 0.8207 (mmt) cc_final: 0.7758 (mmt) REVERT: E 4798 LEU cc_start: 0.8682 (mt) cc_final: 0.8462 (mt) REVERT: E 4952 MET cc_start: 0.6369 (ttt) cc_final: 0.6162 (tmm) REVERT: E 5011 MET cc_start: 0.7504 (mmt) cc_final: 0.7149 (tpp) REVERT: E 5018 ASP cc_start: 0.7486 (t0) cc_final: 0.7061 (t0) REVERT: F 93 PHE cc_start: 0.6857 (t80) cc_final: 0.6651 (t80) REVERT: G 102 GLU cc_start: 0.8457 (tt0) cc_final: 0.7936 (tp30) REVERT: H 15 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6866 (mtt180) REVERT: H 25 ASN cc_start: 0.7944 (m-40) cc_final: 0.7741 (m-40) REVERT: H 130 LYS cc_start: 0.8841 (tptp) cc_final: 0.8174 (pttt) REVERT: H 148 TRP cc_start: 0.8904 (m100) cc_final: 0.8608 (m100) REVERT: H 175 SER cc_start: 0.8772 (p) cc_final: 0.8267 (t) REVERT: H 282 ILE cc_start: 0.5906 (mm) cc_final: 0.5666 (mm) REVERT: H 336 PRO cc_start: 0.7028 (Cg_exo) cc_final: 0.6819 (Cg_endo) REVERT: H 467 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8111 (mmmt) REVERT: H 524 GLU cc_start: 0.7871 (tp30) cc_final: 0.7546 (tp30) REVERT: H 573 GLU cc_start: 0.8466 (mp0) cc_final: 0.7752 (mt-10) REVERT: H 622 THR cc_start: 0.8940 (m) cc_final: 0.8711 (p) REVERT: H 667 MET cc_start: 0.6074 (ttt) cc_final: 0.5873 (tmm) REVERT: H 1100 MET cc_start: 0.8216 (ptp) cc_final: 0.7625 (ptt) REVERT: H 1245 PHE cc_start: 0.8596 (m-80) cc_final: 0.7976 (m-80) REVERT: H 1444 GLU cc_start: 0.7221 (mp0) cc_final: 0.6966 (mp0) REVERT: H 1748 PHE cc_start: 0.8370 (m-80) cc_final: 0.7901 (m-80) REVERT: H 1970 LEU cc_start: 0.7840 (tp) cc_final: 0.7551 (mt) REVERT: H 2013 PHE cc_start: 0.7512 (t80) cc_final: 0.7041 (t80) REVERT: H 2193 TYR cc_start: 0.7542 (m-80) cc_final: 0.7250 (m-80) REVERT: H 2239 TYR cc_start: 0.7641 (m-80) cc_final: 0.7323 (m-80) REVERT: H 2275 ASP cc_start: 0.7841 (t0) cc_final: 0.7586 (t0) REVERT: H 2547 MET cc_start: 0.7355 (tpp) cc_final: 0.6797 (tpt) REVERT: H 2616 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.5873 (mtt180) REVERT: H 3634 MET cc_start: 0.7916 (mmp) cc_final: 0.7697 (mmm) REVERT: H 3719 MET cc_start: 0.7707 (ttm) cc_final: 0.7420 (tpp) REVERT: H 3727 LYS cc_start: 0.8500 (mttm) cc_final: 0.8097 (mmtm) REVERT: H 3789 VAL cc_start: 0.8726 (t) cc_final: 0.8463 (t) REVERT: H 3806 ASP cc_start: 0.6568 (p0) cc_final: 0.5279 (m-30) REVERT: H 3870 MET cc_start: 0.8213 (mtp) cc_final: 0.7903 (mtp) REVERT: H 3900 THR cc_start: 0.8407 (t) cc_final: 0.8195 (m) REVERT: H 4029 ASN cc_start: 0.7412 (t0) cc_final: 0.7108 (t0) REVERT: H 4034 MET cc_start: 0.5079 (mtt) cc_final: 0.4470 (mmt) REVERT: H 4059 MET cc_start: 0.5872 (mtt) cc_final: 0.5563 (mtp) REVERT: H 4187 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6665 (mtt-85) REVERT: H 4668 ILE cc_start: 0.8543 (mm) cc_final: 0.8305 (tp) REVERT: H 4670 LYS cc_start: 0.5204 (ttmt) cc_final: 0.4894 (mmmt) REVERT: H 4796 MET cc_start: 0.8211 (mmt) cc_final: 0.7762 (mmt) REVERT: H 4798 LEU cc_start: 0.8688 (mt) cc_final: 0.8467 (mt) REVERT: H 4952 MET cc_start: 0.6372 (ttt) cc_final: 0.6160 (tmm) REVERT: H 5011 MET cc_start: 0.7498 (mmt) cc_final: 0.7139 (tpp) REVERT: H 5018 ASP cc_start: 0.7487 (t0) cc_final: 0.7051 (t0) REVERT: I 13 PHE cc_start: 0.7708 (m-10) cc_final: 0.7506 (m-80) REVERT: I 93 PHE cc_start: 0.6861 (t80) cc_final: 0.6660 (t80) REVERT: J 102 GLU cc_start: 0.8456 (tt0) cc_final: 0.7941 (tp30) REVERT: K 15 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6864 (mtt180) REVERT: K 25 ASN cc_start: 0.7918 (m-40) cc_final: 0.7716 (m-40) REVERT: K 130 LYS cc_start: 0.8840 (tptp) cc_final: 0.8177 (pttt) REVERT: K 148 TRP cc_start: 0.8905 (m100) cc_final: 0.8607 (m100) REVERT: K 175 SER cc_start: 0.8773 (p) cc_final: 0.8271 (t) REVERT: K 282 ILE cc_start: 0.5902 (mm) cc_final: 0.5665 (mm) REVERT: K 336 PRO cc_start: 0.7010 (Cg_exo) cc_final: 0.6800 (Cg_endo) REVERT: K 467 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8110 (mmmt) REVERT: K 524 GLU cc_start: 0.7869 (tp30) cc_final: 0.7535 (tp30) REVERT: K 573 GLU cc_start: 0.8468 (mp0) cc_final: 0.7754 (mt-10) REVERT: K 622 THR cc_start: 0.8941 (m) cc_final: 0.8713 (p) REVERT: K 667 MET cc_start: 0.6086 (ttt) cc_final: 0.5877 (tmm) REVERT: K 1100 MET cc_start: 0.8222 (ptp) cc_final: 0.7631 (ptt) REVERT: K 1245 PHE cc_start: 0.8594 (m-80) cc_final: 0.7968 (m-80) REVERT: K 1444 GLU cc_start: 0.7225 (mp0) cc_final: 0.6975 (mp0) REVERT: K 1748 PHE cc_start: 0.8372 (m-80) cc_final: 0.7910 (m-80) REVERT: K 1970 LEU cc_start: 0.7835 (tp) cc_final: 0.7539 (mt) REVERT: K 2013 PHE cc_start: 0.7521 (t80) cc_final: 0.7063 (t80) REVERT: K 2193 TYR cc_start: 0.7554 (m-80) cc_final: 0.7255 (m-80) REVERT: K 2239 TYR cc_start: 0.7643 (m-80) cc_final: 0.7325 (m-80) REVERT: K 2261 ASN cc_start: 0.8971 (m110) cc_final: 0.8703 (m110) REVERT: K 2275 ASP cc_start: 0.7841 (t0) cc_final: 0.7608 (t0) REVERT: K 2547 MET cc_start: 0.7330 (tpp) cc_final: 0.6751 (tpt) REVERT: K 2616 ARG cc_start: 0.7014 (mtp-110) cc_final: 0.5978 (mtt180) REVERT: K 3634 MET cc_start: 0.7908 (mmp) cc_final: 0.7686 (mmm) REVERT: K 3719 MET cc_start: 0.7713 (ttm) cc_final: 0.7416 (tpp) REVERT: K 3727 LYS cc_start: 0.8514 (mttm) cc_final: 0.8078 (mmtm) REVERT: K 3789 VAL cc_start: 0.8717 (t) cc_final: 0.8477 (t) REVERT: K 3806 ASP cc_start: 0.6352 (p0) cc_final: 0.5119 (m-30) REVERT: K 3870 MET cc_start: 0.8216 (mtp) cc_final: 0.7913 (mtp) REVERT: K 3900 THR cc_start: 0.8411 (t) cc_final: 0.8198 (m) REVERT: K 4029 ASN cc_start: 0.7406 (t0) cc_final: 0.7127 (t0) REVERT: K 4034 MET cc_start: 0.5110 (mtt) cc_final: 0.4765 (mmt) REVERT: K 4059 MET cc_start: 0.5868 (mtt) cc_final: 0.5559 (mtp) REVERT: K 4179 MET cc_start: 0.7132 (ttt) cc_final: 0.6775 (tmm) REVERT: K 4187 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6677 (mtt-85) REVERT: K 4668 ILE cc_start: 0.8544 (mm) cc_final: 0.8309 (tp) REVERT: K 4670 LYS cc_start: 0.5198 (ttmt) cc_final: 0.4927 (mmmt) REVERT: K 4796 MET cc_start: 0.8205 (mmt) cc_final: 0.7762 (mmt) REVERT: K 4798 LEU cc_start: 0.8680 (mt) cc_final: 0.8456 (mt) REVERT: K 5011 MET cc_start: 0.7492 (mmt) cc_final: 0.7158 (tpp) REVERT: K 5018 ASP cc_start: 0.7485 (t0) cc_final: 0.6801 (t0) REVERT: L 13 PHE cc_start: 0.7704 (m-10) cc_final: 0.7502 (m-80) REVERT: L 93 PHE cc_start: 0.6860 (t80) cc_final: 0.6655 (t80) outliers start: 5 outliers final: 0 residues processed: 3143 average time/residue: 0.8669 time to fit residues: 4782.8691 Evaluate side-chains 2112 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2111 time to evaluate : 8.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1361 optimal weight: 5.9990 chunk 1221 optimal weight: 8.9990 chunk 677 optimal weight: 10.0000 chunk 417 optimal weight: 8.9990 chunk 824 optimal weight: 4.9990 chunk 652 optimal weight: 40.0000 chunk 1263 optimal weight: 2.9990 chunk 488 optimal weight: 0.6980 chunk 768 optimal weight: 3.9990 chunk 940 optimal weight: 4.9990 chunk 1463 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 308 HIS ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS B 681 HIS B 720 HIS B1458 HIS B1776 HIS B1862 GLN B1950 GLN B1973 ASN B2096 GLN B2128 GLN B2194 GLN B2247 ASN B2261 ASN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3423 HIS B3663 HIS ** B3696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3761 GLN B4148 HIS B4572 ASN B4801 HIS B4810 HIS B4855 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 HIS E 308 HIS ** E 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 HIS ** E 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 681 HIS E 720 HIS E1458 HIS E1776 HIS E1862 GLN E1950 GLN E1973 ASN E2096 GLN E2128 GLN E2194 GLN E2247 ASN E2261 ASN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3423 HIS E3663 HIS E3761 GLN E4148 HIS E4572 ASN E4801 HIS E4810 HIS E4855 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 HIS H 308 HIS ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 582 HIS H 681 HIS H 720 HIS H1458 HIS H1776 HIS H1862 GLN H1950 GLN H1973 ASN H2096 GLN H2128 GLN H2194 GLN H2247 ASN H2261 ASN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3423 HIS H3663 HIS ** H3696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3761 GLN H4148 HIS H4572 ASN H4801 HIS H4810 HIS H4855 ASN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 HIS K 308 HIS ** K 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 582 HIS K 681 HIS K 720 HIS K1458 HIS K1776 HIS K1862 GLN K1950 GLN K1973 ASN K2096 GLN K2128 GLN K2194 GLN K2247 ASN K2261 ASN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3663 HIS K3761 GLN K4148 HIS K4572 ASN K4801 HIS K4810 HIS K4855 ASN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.007 0.070 113972 Z= 0.454 Angle : 0.781 17.893 155608 Z= 0.400 Chirality : 0.044 0.188 18776 Planarity : 0.005 0.054 20052 Dihedral : 3.887 21.181 16964 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.07), residues: 14452 helix: 1.10 (0.06), residues: 7264 sheet: -1.40 (0.13), residues: 1424 loop : -1.67 (0.07), residues: 5764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B4714 HIS 0.011 0.002 HIS E1776 PHE 0.048 0.003 PHE B4653 TYR 0.029 0.003 TYR E4793 ARG 0.010 0.001 ARG E1814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2439 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2434 time to evaluate : 9.701 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: A 26 TYR cc_start: 0.8968 (p90) cc_final: 0.8282 (p90) REVERT: A 96 THR cc_start: 0.8972 (m) cc_final: 0.8653 (p) REVERT: A 100 ASP cc_start: 0.7342 (p0) cc_final: 0.7101 (p0) REVERT: B 15 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6837 (mtt180) REVERT: B 18 ASP cc_start: 0.7763 (m-30) cc_final: 0.7327 (m-30) REVERT: B 130 LYS cc_start: 0.8950 (tptp) cc_final: 0.8175 (pttt) REVERT: B 167 ASP cc_start: 0.8503 (m-30) cc_final: 0.8099 (p0) REVERT: B 169 LEU cc_start: 0.8345 (mp) cc_final: 0.8067 (mp) REVERT: B 287 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p) REVERT: B 436 LEU cc_start: 0.7836 (pt) cc_final: 0.7522 (pp) REVERT: B 467 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8309 (mmmt) REVERT: B 573 GLU cc_start: 0.8751 (mp0) cc_final: 0.8079 (pt0) REVERT: B 735 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7049 (mm110) REVERT: B 1100 MET cc_start: 0.8026 (ptp) cc_final: 0.7411 (ptt) REVERT: B 1133 HIS cc_start: 0.7862 (t70) cc_final: 0.7630 (t-90) REVERT: B 1245 PHE cc_start: 0.8925 (m-80) cc_final: 0.8400 (m-80) REVERT: B 1293 LEU cc_start: 0.8836 (mt) cc_final: 0.8620 (mt) REVERT: B 1444 GLU cc_start: 0.7482 (mp0) cc_final: 0.7075 (mp0) REVERT: B 1599 MET cc_start: 0.6755 (ttp) cc_final: 0.6518 (ttt) REVERT: B 1648 MET cc_start: 0.7647 (ttm) cc_final: 0.7352 (ttp) REVERT: B 1854 ILE cc_start: 0.8879 (mm) cc_final: 0.8515 (mm) REVERT: B 1951 GLU cc_start: 0.8796 (tt0) cc_final: 0.8388 (tp30) REVERT: B 2000 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7600 (mtp85) REVERT: B 2009 MET cc_start: 0.7012 (ttm) cc_final: 0.6269 (tpp) REVERT: B 2013 PHE cc_start: 0.8170 (t80) cc_final: 0.7683 (t80) REVERT: B 2154 MET cc_start: 0.8454 (mmm) cc_final: 0.8252 (mmm) REVERT: B 2171 MET cc_start: 0.7636 (tpp) cc_final: 0.7192 (mmt) REVERT: B 2199 MET cc_start: 0.8440 (mmp) cc_final: 0.7748 (mmm) REVERT: B 2212 MET cc_start: 0.7645 (tpp) cc_final: 0.7267 (tpp) REVERT: B 2239 TYR cc_start: 0.8176 (m-80) cc_final: 0.7873 (m-80) REVERT: B 2251 MET cc_start: 0.9373 (mmm) cc_final: 0.8820 (tpt) REVERT: B 2547 MET cc_start: 0.7199 (tpp) cc_final: 0.6910 (tpt) REVERT: B 2616 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.5993 (mtt180) REVERT: B 3831 MET cc_start: 0.7983 (mtp) cc_final: 0.7669 (mtm) REVERT: B 3998 LEU cc_start: 0.8379 (mt) cc_final: 0.8146 (mt) REVERT: B 4013 ASP cc_start: 0.8401 (m-30) cc_final: 0.8145 (m-30) REVERT: B 4032 ASN cc_start: 0.6338 (m-40) cc_final: 0.5984 (t0) REVERT: B 4034 MET cc_start: 0.5837 (mtt) cc_final: 0.5078 (mmt) REVERT: B 4059 MET cc_start: 0.5927 (mtt) cc_final: 0.5723 (mtt) REVERT: B 4179 MET cc_start: 0.8440 (tmm) cc_final: 0.7031 (tmm) REVERT: B 4187 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7101 (mtt-85) REVERT: B 4796 MET cc_start: 0.8140 (mmt) cc_final: 0.7906 (mmt) REVERT: B 4816 MET cc_start: 0.7937 (ppp) cc_final: 0.7534 (ppp) REVERT: B 4997 ASP cc_start: 0.7345 (m-30) cc_final: 0.6917 (m-30) REVERT: D 26 TYR cc_start: 0.8968 (p90) cc_final: 0.8291 (p90) REVERT: D 96 THR cc_start: 0.8976 (m) cc_final: 0.8659 (p) REVERT: D 100 ASP cc_start: 0.7360 (p0) cc_final: 0.7125 (p0) REVERT: E 15 ARG cc_start: 0.7068 (mtt180) cc_final: 0.6836 (mtt180) REVERT: E 18 ASP cc_start: 0.7763 (m-30) cc_final: 0.7346 (m-30) REVERT: E 130 LYS cc_start: 0.8943 (tptp) cc_final: 0.8178 (pttt) REVERT: E 167 ASP cc_start: 0.8473 (m-30) cc_final: 0.8103 (p0) REVERT: E 169 LEU cc_start: 0.8329 (mp) cc_final: 0.8037 (mp) REVERT: E 196 MET cc_start: 0.7348 (mmt) cc_final: 0.7097 (tpp) REVERT: E 287 THR cc_start: 0.8576 (m) cc_final: 0.8336 (p) REVERT: E 436 LEU cc_start: 0.7814 (pt) cc_final: 0.7498 (pp) REVERT: E 467 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8303 (mmmt) REVERT: E 573 GLU cc_start: 0.8736 (mp0) cc_final: 0.8094 (pt0) REVERT: E 735 GLN cc_start: 0.7287 (mm-40) cc_final: 0.7045 (mm110) REVERT: E 1100 MET cc_start: 0.8035 (ptp) cc_final: 0.7421 (ptt) REVERT: E 1152 MET cc_start: 0.7197 (mpp) cc_final: 0.6089 (mpp) REVERT: E 1245 PHE cc_start: 0.8930 (m-80) cc_final: 0.8401 (m-80) REVERT: E 1293 LEU cc_start: 0.8829 (mt) cc_final: 0.8615 (mt) REVERT: E 1444 GLU cc_start: 0.7480 (mp0) cc_final: 0.7069 (mp0) REVERT: E 1599 MET cc_start: 0.6757 (ttp) cc_final: 0.6506 (ttt) REVERT: E 1648 MET cc_start: 0.7649 (ttm) cc_final: 0.7350 (ttp) REVERT: E 1854 ILE cc_start: 0.8874 (mm) cc_final: 0.8494 (mm) REVERT: E 1951 GLU cc_start: 0.8772 (tt0) cc_final: 0.8388 (tp30) REVERT: E 2000 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7603 (mtp85) REVERT: E 2009 MET cc_start: 0.7010 (ttm) cc_final: 0.6258 (tpp) REVERT: E 2013 PHE cc_start: 0.8160 (t80) cc_final: 0.7669 (t80) REVERT: E 2154 MET cc_start: 0.8459 (mmm) cc_final: 0.8249 (mmm) REVERT: E 2171 MET cc_start: 0.7638 (tpp) cc_final: 0.7194 (mmt) REVERT: E 2199 MET cc_start: 0.8438 (mmp) cc_final: 0.7720 (mmm) REVERT: E 2212 MET cc_start: 0.7641 (tpp) cc_final: 0.7262 (tpp) REVERT: E 2239 TYR cc_start: 0.8176 (m-80) cc_final: 0.7878 (m-80) REVERT: E 2251 MET cc_start: 0.9371 (mmm) cc_final: 0.8816 (tpt) REVERT: E 2547 MET cc_start: 0.7190 (tpp) cc_final: 0.6905 (tpt) REVERT: E 2616 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.5989 (mtt180) REVERT: E 3719 MET cc_start: 0.8310 (ttm) cc_final: 0.8102 (tpp) REVERT: E 3727 LYS cc_start: 0.8656 (mttm) cc_final: 0.8387 (ttmm) REVERT: E 3772 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 3831 MET cc_start: 0.7998 (mtp) cc_final: 0.7667 (mtm) REVERT: E 3994 MET cc_start: 0.6172 (tpt) cc_final: 0.5960 (tpt) REVERT: E 3998 LEU cc_start: 0.8376 (mt) cc_final: 0.8027 (mt) REVERT: E 4013 ASP cc_start: 0.8392 (m-30) cc_final: 0.8143 (m-30) REVERT: E 4059 MET cc_start: 0.5932 (mtt) cc_final: 0.5722 (mtt) REVERT: E 4179 MET cc_start: 0.8443 (tmm) cc_final: 0.7025 (tmm) REVERT: E 4187 ARG cc_start: 0.7630 (mtt-85) cc_final: 0.7146 (mtt-85) REVERT: E 4713 TYR cc_start: 0.8456 (t80) cc_final: 0.8198 (t80) REVERT: E 4796 MET cc_start: 0.8143 (mmt) cc_final: 0.7906 (mmt) REVERT: E 4816 MET cc_start: 0.7932 (ppp) cc_final: 0.7530 (ppp) REVERT: E 4952 MET cc_start: 0.6586 (ttt) cc_final: 0.6084 (tmm) REVERT: E 4997 ASP cc_start: 0.7341 (m-30) cc_final: 0.6911 (m-30) REVERT: G 26 TYR cc_start: 0.8966 (p90) cc_final: 0.8285 (p90) REVERT: G 96 THR cc_start: 0.8972 (m) cc_final: 0.8652 (p) REVERT: G 100 ASP cc_start: 0.7352 (p0) cc_final: 0.7121 (p0) REVERT: H 15 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6563 (mtm180) REVERT: H 18 ASP cc_start: 0.7643 (m-30) cc_final: 0.7353 (m-30) REVERT: H 130 LYS cc_start: 0.8943 (tptp) cc_final: 0.8178 (pttt) REVERT: H 167 ASP cc_start: 0.8487 (m-30) cc_final: 0.8117 (p0) REVERT: H 169 LEU cc_start: 0.8320 (mp) cc_final: 0.8043 (mp) REVERT: H 196 MET cc_start: 0.7351 (mmt) cc_final: 0.7096 (tpp) REVERT: H 287 THR cc_start: 0.8584 (m) cc_final: 0.8346 (p) REVERT: H 436 LEU cc_start: 0.7821 (pt) cc_final: 0.7495 (pp) REVERT: H 467 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8305 (mmmt) REVERT: H 573 GLU cc_start: 0.8744 (mp0) cc_final: 0.8096 (pt0) REVERT: H 623 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7746 (tp30) REVERT: H 735 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7042 (mm110) REVERT: H 1100 MET cc_start: 0.8028 (ptp) cc_final: 0.7407 (ptt) REVERT: H 1152 MET cc_start: 0.7193 (mpp) cc_final: 0.6085 (mpp) REVERT: H 1245 PHE cc_start: 0.8932 (m-80) cc_final: 0.8402 (m-80) REVERT: H 1293 LEU cc_start: 0.8825 (mt) cc_final: 0.8606 (mt) REVERT: H 1444 GLU cc_start: 0.7478 (mp0) cc_final: 0.7067 (mp0) REVERT: H 1599 MET cc_start: 0.6753 (ttp) cc_final: 0.6506 (ttt) REVERT: H 1648 MET cc_start: 0.7654 (ttm) cc_final: 0.7347 (ttp) REVERT: H 1854 ILE cc_start: 0.8876 (mm) cc_final: 0.8494 (mm) REVERT: H 1951 GLU cc_start: 0.8826 (tt0) cc_final: 0.8433 (tp30) REVERT: H 2000 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7601 (mtp85) REVERT: H 2009 MET cc_start: 0.7011 (ttm) cc_final: 0.6268 (tpp) REVERT: H 2013 PHE cc_start: 0.8165 (t80) cc_final: 0.7624 (t80) REVERT: H 2154 MET cc_start: 0.8461 (mmm) cc_final: 0.8252 (mmm) REVERT: H 2171 MET cc_start: 0.7642 (tpp) cc_final: 0.7194 (mmt) REVERT: H 2199 MET cc_start: 0.8434 (mmp) cc_final: 0.7714 (mmm) REVERT: H 2212 MET cc_start: 0.7665 (tpp) cc_final: 0.7276 (tpp) REVERT: H 2239 TYR cc_start: 0.8171 (m-80) cc_final: 0.7875 (m-80) REVERT: H 2251 MET cc_start: 0.9372 (mmm) cc_final: 0.8820 (tpt) REVERT: H 2275 ASP cc_start: 0.8159 (t0) cc_final: 0.7952 (t0) REVERT: H 2287 LEU cc_start: 0.8567 (mt) cc_final: 0.8366 (mm) REVERT: H 2547 MET cc_start: 0.7192 (tpp) cc_final: 0.6901 (tpt) REVERT: H 2616 ARG cc_start: 0.6983 (mtp-110) cc_final: 0.5963 (mtt180) REVERT: H 3772 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8037 (mm-30) REVERT: H 3831 MET cc_start: 0.7999 (mtp) cc_final: 0.7674 (mtm) REVERT: H 3998 LEU cc_start: 0.8375 (mt) cc_final: 0.8139 (mt) REVERT: H 4013 ASP cc_start: 0.8390 (m-30) cc_final: 0.8133 (m-30) REVERT: H 4179 MET cc_start: 0.8448 (tmm) cc_final: 0.7025 (tmm) REVERT: H 4187 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7107 (mtt-85) REVERT: H 4796 MET cc_start: 0.8139 (mmt) cc_final: 0.7902 (mmt) REVERT: H 4816 MET cc_start: 0.7934 (ppp) cc_final: 0.7528 (ppp) REVERT: H 4952 MET cc_start: 0.6578 (ttt) cc_final: 0.6078 (tmm) REVERT: H 4997 ASP cc_start: 0.7343 (m-30) cc_final: 0.6925 (m-30) REVERT: J 26 TYR cc_start: 0.8968 (p90) cc_final: 0.8276 (p90) REVERT: J 96 THR cc_start: 0.8971 (m) cc_final: 0.8642 (p) REVERT: J 100 ASP cc_start: 0.7351 (p0) cc_final: 0.7123 (p0) REVERT: K 18 ASP cc_start: 0.7650 (m-30) cc_final: 0.7345 (m-30) REVERT: K 130 LYS cc_start: 0.8945 (tptp) cc_final: 0.8177 (pttt) REVERT: K 167 ASP cc_start: 0.8494 (m-30) cc_final: 0.8112 (p0) REVERT: K 169 LEU cc_start: 0.8321 (mp) cc_final: 0.8045 (mp) REVERT: K 196 MET cc_start: 0.7350 (mmt) cc_final: 0.7089 (tpp) REVERT: K 287 THR cc_start: 0.8589 (m) cc_final: 0.8341 (p) REVERT: K 436 LEU cc_start: 0.7838 (pt) cc_final: 0.7509 (pp) REVERT: K 467 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8306 (mmmt) REVERT: K 573 GLU cc_start: 0.8748 (mp0) cc_final: 0.8094 (pt0) REVERT: K 623 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7744 (tp30) REVERT: K 735 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7036 (mm110) REVERT: K 1100 MET cc_start: 0.8023 (ptp) cc_final: 0.7410 (ptt) REVERT: K 1133 HIS cc_start: 0.7871 (t70) cc_final: 0.7630 (t-90) REVERT: K 1152 MET cc_start: 0.7190 (mpp) cc_final: 0.6075 (mpp) REVERT: K 1245 PHE cc_start: 0.8935 (m-80) cc_final: 0.8408 (m-80) REVERT: K 1293 LEU cc_start: 0.8828 (mt) cc_final: 0.8607 (mt) REVERT: K 1444 GLU cc_start: 0.7484 (mp0) cc_final: 0.7073 (mp0) REVERT: K 1599 MET cc_start: 0.6751 (ttp) cc_final: 0.6514 (ttt) REVERT: K 1648 MET cc_start: 0.7649 (ttm) cc_final: 0.7338 (ttp) REVERT: K 1854 ILE cc_start: 0.8876 (mm) cc_final: 0.8489 (mm) REVERT: K 1951 GLU cc_start: 0.8796 (tt0) cc_final: 0.8391 (tp30) REVERT: K 2000 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7591 (mtp85) REVERT: K 2009 MET cc_start: 0.7091 (ttm) cc_final: 0.6337 (tpp) REVERT: K 2013 PHE cc_start: 0.8161 (t80) cc_final: 0.7682 (t80) REVERT: K 2154 MET cc_start: 0.8458 (mmm) cc_final: 0.8250 (mmm) REVERT: K 2171 MET cc_start: 0.7633 (tpp) cc_final: 0.7187 (mmt) REVERT: K 2199 MET cc_start: 0.8433 (mmp) cc_final: 0.7749 (mmm) REVERT: K 2212 MET cc_start: 0.7609 (tpp) cc_final: 0.7257 (tpp) REVERT: K 2239 TYR cc_start: 0.8166 (m-80) cc_final: 0.7877 (m-80) REVERT: K 2275 ASP cc_start: 0.8184 (t0) cc_final: 0.7930 (t0) REVERT: K 2547 MET cc_start: 0.7189 (tpp) cc_final: 0.6901 (tpt) REVERT: K 2616 ARG cc_start: 0.7089 (mtp-110) cc_final: 0.5986 (mtt180) REVERT: K 3719 MET cc_start: 0.8307 (ttm) cc_final: 0.8104 (tpp) REVERT: K 3727 LYS cc_start: 0.8651 (mttm) cc_final: 0.8378 (ttmm) REVERT: K 3772 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8042 (mm-30) REVERT: K 3831 MET cc_start: 0.8015 (mtp) cc_final: 0.7681 (mtm) REVERT: K 3998 LEU cc_start: 0.8387 (mt) cc_final: 0.8152 (mt) REVERT: K 4013 ASP cc_start: 0.8396 (m-30) cc_final: 0.8136 (m-30) REVERT: K 4032 ASN cc_start: 0.6713 (m-40) cc_final: 0.6300 (t0) REVERT: K 4034 MET cc_start: 0.5941 (mtt) cc_final: 0.5311 (mmt) REVERT: K 4187 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7113 (mtt-85) REVERT: K 4796 MET cc_start: 0.8139 (mmt) cc_final: 0.7901 (mmt) REVERT: K 4816 MET cc_start: 0.7940 (ppp) cc_final: 0.7537 (ppp) REVERT: K 4997 ASP cc_start: 0.7347 (m-30) cc_final: 0.6915 (m-30) outliers start: 5 outliers final: 0 residues processed: 2439 average time/residue: 0.8615 time to fit residues: 3731.6198 Evaluate side-chains 2034 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2034 time to evaluate : 8.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 813 optimal weight: 4.9990 chunk 454 optimal weight: 0.0570 chunk 1218 optimal weight: 1.9990 chunk 996 optimal weight: 0.6980 chunk 403 optimal weight: 10.0000 chunk 1466 optimal weight: 10.0000 chunk 1584 optimal weight: 0.2980 chunk 1306 optimal weight: 10.0000 chunk 1454 optimal weight: 3.9990 chunk 499 optimal weight: 7.9990 chunk 1176 optimal weight: 0.7980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1640 HIS ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1776 HIS B1862 GLN B2096 GLN B2194 GLN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3696 GLN B3766 HIS B3945 ASN B4148 HIS ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 HIS ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1640 HIS ** E1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1776 HIS E1862 GLN E1950 GLN E2096 GLN E2194 GLN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3766 HIS E3945 ASN E4148 HIS ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 350 HIS ** H1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1640 HIS ** H1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1776 HIS H1862 GLN H1950 GLN H2096 GLN H2194 GLN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3766 HIS H3945 ASN H4148 HIS ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS K1640 HIS ** K1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1776 HIS K1862 GLN K1950 GLN K2096 GLN K2194 GLN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3766 HIS K3945 ASN K4148 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 113972 Z= 0.161 Angle : 0.523 9.992 155608 Z= 0.257 Chirality : 0.037 0.168 18776 Planarity : 0.004 0.060 20052 Dihedral : 3.381 17.488 16964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.07), residues: 14452 helix: 1.88 (0.06), residues: 7240 sheet: -1.13 (0.13), residues: 1388 loop : -1.44 (0.07), residues: 5824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 702 HIS 0.009 0.001 HIS E2585 PHE 0.032 0.002 PHE B1549 TYR 0.024 0.001 TYR H4075 ARG 0.019 0.001 ARG H1275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2390 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2390 time to evaluate : 8.661 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: A 102 GLU cc_start: 0.8279 (tt0) cc_final: 0.7738 (tp30) REVERT: B 15 ARG cc_start: 0.6938 (mtt180) cc_final: 0.6534 (mtm180) REVERT: B 18 ASP cc_start: 0.7714 (m-30) cc_final: 0.7217 (m-30) REVERT: B 42 PHE cc_start: 0.7434 (m-80) cc_final: 0.7223 (m-80) REVERT: B 130 LYS cc_start: 0.8787 (tptp) cc_final: 0.8105 (pttt) REVERT: B 167 ASP cc_start: 0.8385 (m-30) cc_final: 0.8050 (p0) REVERT: B 467 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8168 (mmmt) REVERT: B 573 GLU cc_start: 0.8656 (mp0) cc_final: 0.8080 (pt0) REVERT: B 735 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6870 (mm110) REVERT: B 1089 TYR cc_start: 0.8066 (t80) cc_final: 0.7558 (t80) REVERT: B 1100 MET cc_start: 0.8252 (ptp) cc_final: 0.7483 (ptt) REVERT: B 1152 MET cc_start: 0.7083 (mpp) cc_final: 0.6695 (mpp) REVERT: B 1245 PHE cc_start: 0.8879 (m-80) cc_final: 0.8326 (m-80) REVERT: B 1293 LEU cc_start: 0.8504 (mt) cc_final: 0.8253 (mt) REVERT: B 1444 GLU cc_start: 0.7465 (mp0) cc_final: 0.6986 (mp0) REVERT: B 1584 ARG cc_start: 0.5601 (tpp-160) cc_final: 0.5182 (tpp-160) REVERT: B 1648 MET cc_start: 0.7601 (ttm) cc_final: 0.7343 (ttp) REVERT: B 1703 LEU cc_start: 0.8821 (tp) cc_final: 0.8207 (mp) REVERT: B 1721 GLU cc_start: 0.8551 (tt0) cc_final: 0.8026 (tp30) REVERT: B 1854 ILE cc_start: 0.8905 (mm) cc_final: 0.8377 (mm) REVERT: B 1970 LEU cc_start: 0.6954 (tp) cc_final: 0.6613 (tt) REVERT: B 1973 ASN cc_start: 0.7253 (t0) cc_final: 0.7002 (t0) REVERT: B 2000 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7368 (mtp85) REVERT: B 2013 PHE cc_start: 0.8033 (t80) cc_final: 0.7544 (t80) REVERT: B 2171 MET cc_start: 0.7413 (tpp) cc_final: 0.7074 (mmt) REVERT: B 2212 MET cc_start: 0.7473 (tpp) cc_final: 0.6957 (tpt) REVERT: B 2214 ASN cc_start: 0.8115 (m-40) cc_final: 0.7494 (t0) REVERT: B 2239 TYR cc_start: 0.7946 (m-80) cc_final: 0.7716 (m-80) REVERT: B 2247 ASN cc_start: 0.9050 (m110) cc_final: 0.8830 (m110) REVERT: B 2248 GLN cc_start: 0.9111 (tt0) cc_final: 0.8680 (tt0) REVERT: B 2251 MET cc_start: 0.9308 (mmm) cc_final: 0.8681 (tpt) REVERT: B 2319 TYR cc_start: 0.7897 (m-80) cc_final: 0.7496 (m-10) REVERT: B 2461 LEU cc_start: 0.7493 (tp) cc_final: 0.7189 (tp) REVERT: B 2547 MET cc_start: 0.7272 (tpp) cc_final: 0.7007 (tpt) REVERT: B 2616 ARG cc_start: 0.6875 (mtp-110) cc_final: 0.5953 (mtm180) REVERT: B 3438 MET cc_start: 0.6858 (mmp) cc_final: 0.6573 (mmt) REVERT: B 3634 MET cc_start: 0.8139 (mmp) cc_final: 0.7913 (mmm) REVERT: B 3657 TRP cc_start: 0.6775 (m100) cc_final: 0.6091 (m100) REVERT: B 3727 LYS cc_start: 0.8564 (mttm) cc_final: 0.8312 (ttmm) REVERT: B 3806 ASP cc_start: 0.6683 (p0) cc_final: 0.5427 (m-30) REVERT: B 3831 MET cc_start: 0.7764 (mtp) cc_final: 0.7395 (mtm) REVERT: B 3998 LEU cc_start: 0.8173 (mt) cc_final: 0.7905 (mt) REVERT: B 4013 ASP cc_start: 0.8297 (m-30) cc_final: 0.8037 (m-30) REVERT: B 4034 MET cc_start: 0.5162 (mtt) cc_final: 0.4761 (mmm) REVERT: B 4059 MET cc_start: 0.5933 (mtt) cc_final: 0.5725 (mtt) REVERT: B 4179 MET cc_start: 0.8458 (tmm) cc_final: 0.7167 (tmm) REVERT: B 4187 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.6828 (mtt-85) REVERT: B 4995 ASN cc_start: 0.8840 (t0) cc_final: 0.8139 (t0) REVERT: C 1 MET cc_start: 0.7205 (mmm) cc_final: 0.6968 (mtp) REVERT: D 102 GLU cc_start: 0.8280 (tt0) cc_final: 0.7742 (tp30) REVERT: E 15 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6549 (mtm180) REVERT: E 18 ASP cc_start: 0.7756 (m-30) cc_final: 0.7289 (m-30) REVERT: E 130 LYS cc_start: 0.8780 (tptp) cc_final: 0.8108 (pttt) REVERT: E 167 ASP cc_start: 0.8361 (m-30) cc_final: 0.8056 (p0) REVERT: E 196 MET cc_start: 0.7408 (mmt) cc_final: 0.7197 (tpp) REVERT: E 467 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8159 (mmmt) REVERT: E 573 GLU cc_start: 0.8662 (mp0) cc_final: 0.8085 (pt0) REVERT: E 735 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6866 (mm110) REVERT: E 1100 MET cc_start: 0.8256 (ptp) cc_final: 0.7493 (ptt) REVERT: E 1245 PHE cc_start: 0.8879 (m-80) cc_final: 0.8321 (m-80) REVERT: E 1256 GLU cc_start: 0.8262 (pt0) cc_final: 0.7825 (pm20) REVERT: E 1293 LEU cc_start: 0.8535 (mt) cc_final: 0.8269 (mt) REVERT: E 1444 GLU cc_start: 0.7481 (mp0) cc_final: 0.6989 (mp0) REVERT: E 1584 ARG cc_start: 0.5599 (tpp-160) cc_final: 0.5185 (tpp-160) REVERT: E 1648 MET cc_start: 0.7604 (ttm) cc_final: 0.7340 (ttp) REVERT: E 1703 LEU cc_start: 0.8817 (tp) cc_final: 0.8195 (mp) REVERT: E 1854 ILE cc_start: 0.8853 (mm) cc_final: 0.8392 (mm) REVERT: E 1970 LEU cc_start: 0.6987 (tp) cc_final: 0.6648 (tt) REVERT: E 1973 ASN cc_start: 0.7245 (t0) cc_final: 0.6998 (t0) REVERT: E 2000 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7361 (mtp85) REVERT: E 2013 PHE cc_start: 0.8043 (t80) cc_final: 0.7573 (t80) REVERT: E 2171 MET cc_start: 0.7478 (tpp) cc_final: 0.7137 (mmt) REVERT: E 2212 MET cc_start: 0.7471 (tpp) cc_final: 0.6955 (tpt) REVERT: E 2214 ASN cc_start: 0.8119 (m-40) cc_final: 0.7490 (t0) REVERT: E 2239 TYR cc_start: 0.7947 (m-80) cc_final: 0.7721 (m-80) REVERT: E 2247 ASN cc_start: 0.9057 (m110) cc_final: 0.8833 (m110) REVERT: E 2248 GLN cc_start: 0.9113 (tt0) cc_final: 0.8677 (tt0) REVERT: E 2251 MET cc_start: 0.9301 (mmm) cc_final: 0.8676 (tpt) REVERT: E 2319 TYR cc_start: 0.7895 (m-80) cc_final: 0.7493 (m-10) REVERT: E 2444 ILE cc_start: 0.9185 (mt) cc_final: 0.8967 (mm) REVERT: E 2461 LEU cc_start: 0.7514 (tp) cc_final: 0.7215 (tp) REVERT: E 2547 MET cc_start: 0.7270 (tpp) cc_final: 0.7009 (tpt) REVERT: E 2616 ARG cc_start: 0.6870 (mtp-110) cc_final: 0.5949 (mtm180) REVERT: E 3438 MET cc_start: 0.6851 (mmp) cc_final: 0.6562 (mmt) REVERT: E 3634 MET cc_start: 0.8150 (mmp) cc_final: 0.7929 (mmm) REVERT: E 3657 TRP cc_start: 0.6804 (m100) cc_final: 0.6126 (m100) REVERT: E 3719 MET cc_start: 0.8095 (ttm) cc_final: 0.7799 (tpp) REVERT: E 3725 MET cc_start: 0.6554 (mtp) cc_final: 0.6305 (mtm) REVERT: E 3727 LYS cc_start: 0.8562 (mttm) cc_final: 0.8309 (ttmm) REVERT: E 3772 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7916 (mm-30) REVERT: E 3806 ASP cc_start: 0.6723 (p0) cc_final: 0.5428 (m-30) REVERT: E 3831 MET cc_start: 0.7774 (mtp) cc_final: 0.7394 (mtm) REVERT: E 3998 LEU cc_start: 0.8167 (mt) cc_final: 0.7852 (mt) REVERT: E 4013 ASP cc_start: 0.8284 (m-30) cc_final: 0.8048 (m-30) REVERT: E 4034 MET cc_start: 0.5607 (mtp) cc_final: 0.4806 (mmt) REVERT: E 4059 MET cc_start: 0.5915 (mtt) cc_final: 0.5698 (mtt) REVERT: E 4179 MET cc_start: 0.8474 (tmm) cc_final: 0.7157 (tmm) REVERT: E 4187 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.6786 (mtt-85) REVERT: E 4952 MET cc_start: 0.6522 (ttt) cc_final: 0.6053 (tmm) REVERT: E 4995 ASN cc_start: 0.8832 (t0) cc_final: 0.8578 (t0) REVERT: F 1 MET cc_start: 0.7209 (mmm) cc_final: 0.6965 (mtp) REVERT: G 102 GLU cc_start: 0.8284 (tt0) cc_final: 0.7748 (tp30) REVERT: H 15 ARG cc_start: 0.6902 (mtt180) cc_final: 0.6550 (mtm180) REVERT: H 18 ASP cc_start: 0.7703 (m-30) cc_final: 0.7275 (m-30) REVERT: H 130 LYS cc_start: 0.8781 (tptp) cc_final: 0.8102 (pttt) REVERT: H 167 ASP cc_start: 0.8385 (m-30) cc_final: 0.8068 (p0) REVERT: H 196 MET cc_start: 0.7417 (mmt) cc_final: 0.7204 (tpp) REVERT: H 467 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8160 (mmmt) REVERT: H 573 GLU cc_start: 0.8645 (mp0) cc_final: 0.8075 (pt0) REVERT: H 735 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6870 (mm110) REVERT: H 1100 MET cc_start: 0.8250 (ptp) cc_final: 0.7483 (ptt) REVERT: H 1245 PHE cc_start: 0.8884 (m-80) cc_final: 0.8323 (m-80) REVERT: H 1256 GLU cc_start: 0.8271 (pt0) cc_final: 0.7822 (pm20) REVERT: H 1293 LEU cc_start: 0.8532 (mt) cc_final: 0.8254 (mt) REVERT: H 1444 GLU cc_start: 0.7476 (mp0) cc_final: 0.6992 (mp0) REVERT: H 1584 ARG cc_start: 0.5602 (tpp-160) cc_final: 0.5194 (tpp-160) REVERT: H 1648 MET cc_start: 0.7605 (ttm) cc_final: 0.7339 (ttp) REVERT: H 1703 LEU cc_start: 0.8825 (tp) cc_final: 0.8191 (mp) REVERT: H 1854 ILE cc_start: 0.8852 (mm) cc_final: 0.8393 (mm) REVERT: H 1970 LEU cc_start: 0.6964 (tp) cc_final: 0.6618 (tt) REVERT: H 1973 ASN cc_start: 0.7258 (t0) cc_final: 0.7003 (t0) REVERT: H 2000 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7362 (mtp85) REVERT: H 2013 PHE cc_start: 0.8030 (t80) cc_final: 0.7531 (t80) REVERT: H 2171 MET cc_start: 0.7482 (tpp) cc_final: 0.7137 (mmt) REVERT: H 2212 MET cc_start: 0.7480 (tpp) cc_final: 0.7070 (tpp) REVERT: H 2214 ASN cc_start: 0.8103 (m-40) cc_final: 0.7444 (t0) REVERT: H 2239 TYR cc_start: 0.7944 (m-80) cc_final: 0.7710 (m-80) REVERT: H 2247 ASN cc_start: 0.9063 (m110) cc_final: 0.8846 (m110) REVERT: H 2248 GLN cc_start: 0.9135 (tt0) cc_final: 0.8704 (tt0) REVERT: H 2251 MET cc_start: 0.9306 (mmm) cc_final: 0.8691 (tpt) REVERT: H 2275 ASP cc_start: 0.8013 (t0) cc_final: 0.7797 (t0) REVERT: H 2319 TYR cc_start: 0.7895 (m-80) cc_final: 0.7480 (m-10) REVERT: H 2461 LEU cc_start: 0.7515 (tp) cc_final: 0.7206 (tp) REVERT: H 2547 MET cc_start: 0.7263 (tpp) cc_final: 0.7006 (tpt) REVERT: H 2616 ARG cc_start: 0.6889 (mtp-110) cc_final: 0.5881 (mtm180) REVERT: H 3438 MET cc_start: 0.6859 (mmp) cc_final: 0.6578 (mmt) REVERT: H 3634 MET cc_start: 0.8150 (mmp) cc_final: 0.7930 (mmm) REVERT: H 3657 TRP cc_start: 0.6781 (m100) cc_final: 0.6112 (m100) REVERT: H 3725 MET cc_start: 0.6530 (mtp) cc_final: 0.6287 (mtm) REVERT: H 3727 LYS cc_start: 0.8574 (mttm) cc_final: 0.8329 (ttmm) REVERT: H 3772 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8204 (mm-30) REVERT: H 3800 LEU cc_start: 0.8674 (mp) cc_final: 0.8455 (mp) REVERT: H 3806 ASP cc_start: 0.6677 (p0) cc_final: 0.5428 (m-30) REVERT: H 3831 MET cc_start: 0.7773 (mtp) cc_final: 0.7410 (mtm) REVERT: H 3998 LEU cc_start: 0.8177 (mt) cc_final: 0.7902 (mt) REVERT: H 4013 ASP cc_start: 0.8291 (m-30) cc_final: 0.8031 (m-30) REVERT: H 4034 MET cc_start: 0.5593 (mtp) cc_final: 0.4788 (mmt) REVERT: H 4179 MET cc_start: 0.8481 (tmm) cc_final: 0.7157 (tmm) REVERT: H 4187 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.6777 (mtt-85) REVERT: H 4952 MET cc_start: 0.6514 (ttt) cc_final: 0.6051 (tmm) REVERT: H 4995 ASN cc_start: 0.8829 (t0) cc_final: 0.8115 (t0) REVERT: I 1 MET cc_start: 0.7190 (mmm) cc_final: 0.6966 (mtp) REVERT: J 102 GLU cc_start: 0.8275 (tt0) cc_final: 0.7634 (mm-30) REVERT: K 15 ARG cc_start: 0.6831 (mtt180) cc_final: 0.6441 (mtm180) REVERT: K 18 ASP cc_start: 0.7703 (m-30) cc_final: 0.7300 (m-30) REVERT: K 130 LYS cc_start: 0.8781 (tptp) cc_final: 0.8106 (pttt) REVERT: K 167 ASP cc_start: 0.8382 (m-30) cc_final: 0.8067 (p0) REVERT: K 196 MET cc_start: 0.7404 (mmt) cc_final: 0.7171 (tpp) REVERT: K 467 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8157 (mmmt) REVERT: K 573 GLU cc_start: 0.8644 (mp0) cc_final: 0.8066 (pt0) REVERT: K 735 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6862 (mm110) REVERT: K 1100 MET cc_start: 0.8247 (ptp) cc_final: 0.7492 (ptt) REVERT: K 1245 PHE cc_start: 0.8885 (m-80) cc_final: 0.8336 (m-80) REVERT: K 1256 GLU cc_start: 0.8266 (pt0) cc_final: 0.7820 (pm20) REVERT: K 1293 LEU cc_start: 0.8531 (mt) cc_final: 0.8251 (mt) REVERT: K 1444 GLU cc_start: 0.7484 (mp0) cc_final: 0.6998 (mp0) REVERT: K 1584 ARG cc_start: 0.5606 (tpp-160) cc_final: 0.5201 (tpp-160) REVERT: K 1703 LEU cc_start: 0.8823 (tp) cc_final: 0.8207 (mp) REVERT: K 1854 ILE cc_start: 0.8859 (mm) cc_final: 0.8402 (mm) REVERT: K 1970 LEU cc_start: 0.6956 (tp) cc_final: 0.6614 (tt) REVERT: K 1973 ASN cc_start: 0.7252 (t0) cc_final: 0.6996 (t0) REVERT: K 2000 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7367 (mtp85) REVERT: K 2013 PHE cc_start: 0.8043 (t80) cc_final: 0.7509 (t80) REVERT: K 2171 MET cc_start: 0.7476 (tpp) cc_final: 0.7141 (mmt) REVERT: K 2212 MET cc_start: 0.7445 (tpp) cc_final: 0.6972 (tpt) REVERT: K 2239 TYR cc_start: 0.7966 (m-80) cc_final: 0.7716 (m-80) REVERT: K 2248 GLN cc_start: 0.9095 (tt0) cc_final: 0.8551 (tt0) REVERT: K 2275 ASP cc_start: 0.8068 (t0) cc_final: 0.7840 (t0) REVERT: K 2319 TYR cc_start: 0.7898 (m-80) cc_final: 0.7487 (m-10) REVERT: K 2461 LEU cc_start: 0.7513 (tp) cc_final: 0.7208 (tp) REVERT: K 2547 MET cc_start: 0.7267 (tpp) cc_final: 0.7001 (tpt) REVERT: K 2616 ARG cc_start: 0.6873 (mtp-110) cc_final: 0.5957 (mtm180) REVERT: K 3438 MET cc_start: 0.6871 (mmp) cc_final: 0.6587 (mmt) REVERT: K 3634 MET cc_start: 0.8142 (mmp) cc_final: 0.7916 (mmm) REVERT: K 3719 MET cc_start: 0.8061 (ttm) cc_final: 0.7761 (tpp) REVERT: K 3725 MET cc_start: 0.6551 (mtp) cc_final: 0.6294 (mtm) REVERT: K 3727 LYS cc_start: 0.8559 (mttm) cc_final: 0.8304 (ttmm) REVERT: K 3753 MET cc_start: 0.7129 (tpp) cc_final: 0.6506 (tpt) REVERT: K 3772 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8197 (mm-30) REVERT: K 3806 ASP cc_start: 0.6722 (p0) cc_final: 0.5429 (m-30) REVERT: K 3831 MET cc_start: 0.7788 (mtp) cc_final: 0.7409 (mtm) REVERT: K 3998 LEU cc_start: 0.8185 (mt) cc_final: 0.7923 (mt) REVERT: K 4013 ASP cc_start: 0.8282 (m-30) cc_final: 0.8039 (m-30) REVERT: K 4032 ASN cc_start: 0.6210 (m-40) cc_final: 0.5991 (t0) REVERT: K 4034 MET cc_start: 0.5499 (mtt) cc_final: 0.4813 (mmt) REVERT: K 4179 MET cc_start: 0.8225 (tmm) cc_final: 0.7202 (tmm) REVERT: K 4187 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.6798 (mtt-85) REVERT: K 4796 MET cc_start: 0.8124 (mmt) cc_final: 0.7729 (mmt) REVERT: L 1 MET cc_start: 0.7196 (mmm) cc_final: 0.6964 (mtp) outliers start: 0 outliers final: 0 residues processed: 2390 average time/residue: 0.8604 time to fit residues: 3663.5824 Evaluate side-chains 2045 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2045 time to evaluate : 8.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1448 optimal weight: 30.0000 chunk 1102 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 699 optimal weight: 8.9990 chunk 984 optimal weight: 2.9990 chunk 1471 optimal weight: 30.0000 chunk 1558 optimal weight: 0.9980 chunk 768 optimal weight: 4.9990 chunk 1394 optimal weight: 2.9990 chunk 419 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 255 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN B1229 ASN B1254 HIS B1484 HIS ** B1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1611 HIS B1629 GLN ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1862 GLN B1950 GLN B2194 GLN B2247 ASN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4785 ASN B4804 ASN B4855 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 255 HIS ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1229 ASN E1254 HIS E1484 HIS ** E1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1611 HIS ** E1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1862 GLN E1950 GLN E2194 GLN E2247 ASN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4785 ASN E4804 ASN E4855 ASN E5001 HIS ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN H 255 HIS ** H 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1229 ASN H1254 HIS H1484 HIS ** H1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1862 GLN H1950 GLN H2108 GLN H2194 GLN H2247 ASN H2261 ASN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H4785 ASN H4804 ASN H4855 ASN H5001 HIS ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN K 255 HIS K1229 ASN K1254 HIS K1484 HIS ** K1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1862 GLN K1950 GLN K2194 GLN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K4785 ASN K4804 ASN K4855 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 113972 Z= 0.420 Angle : 0.755 13.750 155608 Z= 0.384 Chirality : 0.044 0.204 18776 Planarity : 0.005 0.056 20052 Dihedral : 4.347 23.124 16964 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.07), residues: 14452 helix: 1.38 (0.06), residues: 7196 sheet: -1.10 (0.13), residues: 1392 loop : -1.61 (0.07), residues: 5864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K4714 HIS 0.010 0.002 HIS K4884 PHE 0.034 0.003 PHE L 13 TYR 0.039 0.003 TYR E4986 ARG 0.008 0.001 ARG K5027 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2325 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2316 time to evaluate : 9.056 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: B 15 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6516 (mtm180) REVERT: B 18 ASP cc_start: 0.7744 (m-30) cc_final: 0.7316 (m-30) REVERT: B 167 ASP cc_start: 0.8904 (m-30) cc_final: 0.8430 (p0) REVERT: B 192 ASP cc_start: 0.8403 (m-30) cc_final: 0.8175 (m-30) REVERT: B 418 LEU cc_start: 0.8674 (tt) cc_final: 0.8434 (tp) REVERT: B 467 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8215 (mmmt) REVERT: B 573 GLU cc_start: 0.8731 (mp0) cc_final: 0.8173 (pt0) REVERT: B 710 ASP cc_start: 0.8169 (m-30) cc_final: 0.7845 (m-30) REVERT: B 735 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7066 (mm110) REVERT: B 800 PHE cc_start: 0.7928 (m-80) cc_final: 0.7565 (m-80) REVERT: B 847 SER cc_start: 0.7519 (t) cc_final: 0.7258 (p) REVERT: B 1089 TYR cc_start: 0.8256 (t80) cc_final: 0.7902 (t80) REVERT: B 1100 MET cc_start: 0.8271 (ptp) cc_final: 0.7589 (ptt) REVERT: B 1141 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7351 (ptp-170) REVERT: B 1152 MET cc_start: 0.7720 (mpp) cc_final: 0.7317 (mpp) REVERT: B 1293 LEU cc_start: 0.8544 (mt) cc_final: 0.8224 (mp) REVERT: B 1444 GLU cc_start: 0.7515 (mp0) cc_final: 0.7044 (mp0) REVERT: B 1573 MET cc_start: 0.6529 (tpp) cc_final: 0.6202 (mmt) REVERT: B 1584 ARG cc_start: 0.6059 (tpp-160) cc_final: 0.4964 (tpp-160) REVERT: B 1601 MET cc_start: 0.8455 (tpp) cc_final: 0.7375 (mtm) REVERT: B 1648 MET cc_start: 0.7813 (ttm) cc_final: 0.7601 (ttp) REVERT: B 1951 GLU cc_start: 0.8711 (tt0) cc_final: 0.8487 (tp30) REVERT: B 2000 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7310 (mtp85) REVERT: B 2171 MET cc_start: 0.7898 (tpp) cc_final: 0.7679 (tpt) REVERT: B 2212 MET cc_start: 0.7778 (tpp) cc_final: 0.7449 (tpp) REVERT: B 2239 TYR cc_start: 0.8203 (m-80) cc_final: 0.7968 (m-80) REVERT: B 2319 TYR cc_start: 0.7936 (m-80) cc_final: 0.7484 (m-10) REVERT: B 2616 ARG cc_start: 0.6969 (mtp-110) cc_final: 0.5915 (mtm180) REVERT: B 3438 MET cc_start: 0.6761 (mmp) cc_final: 0.6413 (mmp) REVERT: B 3664 SER cc_start: 0.8996 (m) cc_final: 0.8591 (t) REVERT: B 3831 MET cc_start: 0.7948 (mtp) cc_final: 0.7715 (mtm) REVERT: B 4013 ASP cc_start: 0.8411 (m-30) cc_final: 0.8171 (m-30) REVERT: B 4029 ASN cc_start: 0.7512 (t0) cc_final: 0.7275 (t0) REVERT: B 4034 MET cc_start: 0.5812 (mtt) cc_final: 0.5474 (mtt) REVERT: B 4059 MET cc_start: 0.5530 (mtt) cc_final: 0.5188 (mtt) REVERT: B 4179 MET cc_start: 0.8505 (tmm) cc_final: 0.7182 (tmm) REVERT: B 4187 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7297 (mtt-85) REVERT: B 4796 MET cc_start: 0.8061 (mmt) cc_final: 0.7768 (mmt) REVERT: B 4802 TYR cc_start: 0.6895 (t80) cc_final: 0.6436 (t80) REVERT: B 4997 ASP cc_start: 0.7592 (m-30) cc_final: 0.7369 (m-30) REVERT: E 15 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6558 (mtm180) REVERT: E 18 ASP cc_start: 0.7691 (m-30) cc_final: 0.7268 (m-30) REVERT: E 167 ASP cc_start: 0.8894 (m-30) cc_final: 0.8462 (p0) REVERT: E 192 ASP cc_start: 0.8402 (m-30) cc_final: 0.8174 (m-30) REVERT: E 248 GLU cc_start: 0.8153 (pt0) cc_final: 0.7888 (pt0) REVERT: E 418 LEU cc_start: 0.8670 (tt) cc_final: 0.8435 (tp) REVERT: E 467 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8209 (mmmt) REVERT: E 573 GLU cc_start: 0.8722 (mp0) cc_final: 0.8167 (pt0) REVERT: E 710 ASP cc_start: 0.8162 (m-30) cc_final: 0.7842 (m-30) REVERT: E 735 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7053 (mm110) REVERT: E 847 SER cc_start: 0.7521 (t) cc_final: 0.7262 (p) REVERT: E 1089 TYR cc_start: 0.8199 (t80) cc_final: 0.7703 (t80) REVERT: E 1100 MET cc_start: 0.8278 (ptp) cc_final: 0.7584 (ptt) REVERT: E 1141 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7363 (ptp-170) REVERT: E 1152 MET cc_start: 0.7451 (mpp) cc_final: 0.6940 (mpp) REVERT: E 1245 PHE cc_start: 0.9120 (m-80) cc_final: 0.8402 (m-80) REVERT: E 1256 GLU cc_start: 0.8187 (pt0) cc_final: 0.7723 (pm20) REVERT: E 1293 LEU cc_start: 0.8582 (mt) cc_final: 0.8270 (mp) REVERT: E 1444 GLU cc_start: 0.7518 (mp0) cc_final: 0.7032 (mp0) REVERT: E 1573 MET cc_start: 0.6520 (tpp) cc_final: 0.6202 (mmt) REVERT: E 1584 ARG cc_start: 0.6069 (tpp-160) cc_final: 0.4979 (tpp-160) REVERT: E 1601 MET cc_start: 0.8455 (tpp) cc_final: 0.7415 (mtm) REVERT: E 1648 MET cc_start: 0.7811 (ttm) cc_final: 0.7602 (ttp) REVERT: E 1930 MET cc_start: 0.8008 (ttt) cc_final: 0.7753 (ttt) REVERT: E 2000 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7294 (mtp85) REVERT: E 2171 MET cc_start: 0.7900 (tpp) cc_final: 0.7677 (tpt) REVERT: E 2212 MET cc_start: 0.7780 (tpp) cc_final: 0.7446 (tpp) REVERT: E 2239 TYR cc_start: 0.8210 (m-80) cc_final: 0.7977 (m-80) REVERT: E 2319 TYR cc_start: 0.7946 (m-80) cc_final: 0.7495 (m-10) REVERT: E 2616 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.5940 (mtm180) REVERT: E 3438 MET cc_start: 0.6762 (mmp) cc_final: 0.6442 (mmp) REVERT: E 3664 SER cc_start: 0.8998 (m) cc_final: 0.8587 (t) REVERT: E 3831 MET cc_start: 0.7960 (mtp) cc_final: 0.7728 (mtm) REVERT: E 4013 ASP cc_start: 0.8402 (m-30) cc_final: 0.8172 (m-30) REVERT: E 4034 MET cc_start: 0.5918 (mtp) cc_final: 0.5024 (mmt) REVERT: E 4059 MET cc_start: 0.5602 (mtt) cc_final: 0.5147 (mtt) REVERT: E 4179 MET cc_start: 0.8511 (tmm) cc_final: 0.7183 (tmm) REVERT: E 4187 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7394 (mtt-85) REVERT: E 4796 MET cc_start: 0.8064 (mmt) cc_final: 0.7771 (mmt) REVERT: E 4802 TYR cc_start: 0.6884 (t80) cc_final: 0.6423 (t80) REVERT: E 4997 ASP cc_start: 0.7628 (m-30) cc_final: 0.7409 (m-30) REVERT: H 15 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6586 (mtm180) REVERT: H 18 ASP cc_start: 0.7704 (m-30) cc_final: 0.7265 (m-30) REVERT: H 192 ASP cc_start: 0.8396 (m-30) cc_final: 0.8180 (m-30) REVERT: H 248 GLU cc_start: 0.8172 (pt0) cc_final: 0.7904 (pt0) REVERT: H 418 LEU cc_start: 0.8674 (tt) cc_final: 0.8421 (tp) REVERT: H 467 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8210 (mmmt) REVERT: H 573 GLU cc_start: 0.8683 (mp0) cc_final: 0.8150 (pt0) REVERT: H 710 ASP cc_start: 0.8162 (m-30) cc_final: 0.7840 (m-30) REVERT: H 735 GLN cc_start: 0.7345 (mm-40) cc_final: 0.7049 (mm110) REVERT: H 847 SER cc_start: 0.7529 (t) cc_final: 0.7273 (p) REVERT: H 1100 MET cc_start: 0.8274 (ptp) cc_final: 0.7601 (ptt) REVERT: H 1141 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7365 (ptp-170) REVERT: H 1245 PHE cc_start: 0.9121 (m-80) cc_final: 0.8400 (m-80) REVERT: H 1256 GLU cc_start: 0.8178 (pt0) cc_final: 0.7721 (pm20) REVERT: H 1293 LEU cc_start: 0.8578 (mt) cc_final: 0.8265 (mp) REVERT: H 1444 GLU cc_start: 0.7526 (mp0) cc_final: 0.7040 (mp0) REVERT: H 1573 MET cc_start: 0.6536 (tpp) cc_final: 0.6203 (mmt) REVERT: H 1584 ARG cc_start: 0.6071 (tpp-160) cc_final: 0.4975 (tpp-160) REVERT: H 1601 MET cc_start: 0.8448 (tpp) cc_final: 0.7410 (mtm) REVERT: H 1648 MET cc_start: 0.7813 (ttm) cc_final: 0.7597 (ttp) REVERT: H 1930 MET cc_start: 0.7970 (ttt) cc_final: 0.7703 (ttt) REVERT: H 2000 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7295 (mtp85) REVERT: H 2171 MET cc_start: 0.7892 (tpp) cc_final: 0.7675 (tpt) REVERT: H 2212 MET cc_start: 0.7844 (tpp) cc_final: 0.7492 (tpp) REVERT: H 2239 TYR cc_start: 0.8207 (m-80) cc_final: 0.7973 (m-80) REVERT: H 2275 ASP cc_start: 0.8144 (t0) cc_final: 0.7933 (t0) REVERT: H 2319 TYR cc_start: 0.7942 (m-80) cc_final: 0.7486 (m-10) REVERT: H 2616 ARG cc_start: 0.7028 (mtp-110) cc_final: 0.5895 (mtm180) REVERT: H 3438 MET cc_start: 0.6776 (mmp) cc_final: 0.6463 (mmp) REVERT: H 3664 SER cc_start: 0.9005 (m) cc_final: 0.8600 (t) REVERT: H 3831 MET cc_start: 0.7962 (mtp) cc_final: 0.7692 (mtm) REVERT: H 4013 ASP cc_start: 0.8406 (m-30) cc_final: 0.8178 (m-30) REVERT: H 4034 MET cc_start: 0.5917 (mtp) cc_final: 0.5024 (mmt) REVERT: H 4179 MET cc_start: 0.8537 (tmm) cc_final: 0.7230 (tmm) REVERT: H 4187 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7392 (mtt-85) REVERT: H 4796 MET cc_start: 0.8059 (mmt) cc_final: 0.7760 (mmt) REVERT: H 4802 TYR cc_start: 0.6903 (t80) cc_final: 0.6437 (t80) REVERT: H 4980 GLU cc_start: 0.7492 (pm20) cc_final: 0.7289 (pm20) REVERT: H 4997 ASP cc_start: 0.7630 (m-30) cc_final: 0.7412 (m-30) REVERT: K 15 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6548 (mtm180) REVERT: K 18 ASP cc_start: 0.7724 (m-30) cc_final: 0.7312 (m-30) REVERT: K 192 ASP cc_start: 0.8410 (m-30) cc_final: 0.8179 (m-30) REVERT: K 248 GLU cc_start: 0.8154 (pt0) cc_final: 0.7895 (pt0) REVERT: K 403 MET cc_start: 0.8674 (mtt) cc_final: 0.8470 (mtm) REVERT: K 418 LEU cc_start: 0.8664 (tt) cc_final: 0.8409 (tp) REVERT: K 467 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8214 (mmmt) REVERT: K 573 GLU cc_start: 0.8692 (mp0) cc_final: 0.8150 (pt0) REVERT: K 710 ASP cc_start: 0.8168 (m-30) cc_final: 0.7852 (m-30) REVERT: K 735 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7054 (mm110) REVERT: K 847 SER cc_start: 0.7533 (t) cc_final: 0.7278 (p) REVERT: K 1089 TYR cc_start: 0.8197 (t80) cc_final: 0.7712 (t80) REVERT: K 1100 MET cc_start: 0.8275 (ptp) cc_final: 0.7607 (ptt) REVERT: K 1141 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7349 (ptp-170) REVERT: K 1152 MET cc_start: 0.7459 (mpp) cc_final: 0.6940 (mpp) REVERT: K 1245 PHE cc_start: 0.9119 (m-80) cc_final: 0.8413 (m-80) REVERT: K 1256 GLU cc_start: 0.8175 (pt0) cc_final: 0.7733 (pm20) REVERT: K 1293 LEU cc_start: 0.8581 (mt) cc_final: 0.8271 (mp) REVERT: K 1444 GLU cc_start: 0.7520 (mp0) cc_final: 0.7035 (mp0) REVERT: K 1573 MET cc_start: 0.6541 (tpp) cc_final: 0.6211 (mmt) REVERT: K 1584 ARG cc_start: 0.6075 (tpp-160) cc_final: 0.4993 (tpp-160) REVERT: K 1601 MET cc_start: 0.8442 (tpp) cc_final: 0.7420 (mtm) REVERT: K 1930 MET cc_start: 0.8017 (ttt) cc_final: 0.7758 (ttt) REVERT: K 2000 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7296 (mtp85) REVERT: K 2171 MET cc_start: 0.7970 (tpp) cc_final: 0.7737 (tpt) REVERT: K 2212 MET cc_start: 0.7594 (tpp) cc_final: 0.7328 (tpp) REVERT: K 2239 TYR cc_start: 0.8221 (m-80) cc_final: 0.7983 (m-80) REVERT: K 2251 MET cc_start: 0.9468 (mmm) cc_final: 0.8990 (tpt) REVERT: K 2275 ASP cc_start: 0.8120 (t0) cc_final: 0.7918 (t0) REVERT: K 2319 TYR cc_start: 0.7926 (m-80) cc_final: 0.7459 (m-10) REVERT: K 2616 ARG cc_start: 0.6965 (mtp-110) cc_final: 0.5915 (mtm180) REVERT: K 3438 MET cc_start: 0.6778 (mmp) cc_final: 0.6423 (mmp) REVERT: K 3664 SER cc_start: 0.9000 (m) cc_final: 0.8600 (t) REVERT: K 3753 MET cc_start: 0.6797 (tpp) cc_final: 0.6356 (tpt) REVERT: K 3831 MET cc_start: 0.7974 (mtp) cc_final: 0.7715 (mtm) REVERT: K 4013 ASP cc_start: 0.8399 (m-30) cc_final: 0.8175 (m-30) REVERT: K 4029 ASN cc_start: 0.7558 (t0) cc_final: 0.7324 (t0) REVERT: K 4032 ASN cc_start: 0.6597 (m-40) cc_final: 0.6102 (t0) REVERT: K 4034 MET cc_start: 0.5597 (mtt) cc_final: 0.5013 (mmt) REVERT: K 4168 TYR cc_start: 0.8217 (t80) cc_final: 0.7947 (t80) REVERT: K 4179 MET cc_start: 0.8428 (tmm) cc_final: 0.7184 (tmm) REVERT: K 4187 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7416 (mtt-85) REVERT: K 4796 MET cc_start: 0.8065 (mmt) cc_final: 0.7778 (mmt) REVERT: K 4802 TYR cc_start: 0.6896 (t80) cc_final: 0.6437 (t80) REVERT: K 4997 ASP cc_start: 0.7721 (m-30) cc_final: 0.7481 (m-30) outliers start: 9 outliers final: 4 residues processed: 2325 average time/residue: 0.8706 time to fit residues: 3617.6315 Evaluate side-chains 1995 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1991 time to evaluate : 8.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1297 optimal weight: 6.9990 chunk 884 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 1160 optimal weight: 2.9990 chunk 642 optimal weight: 50.0000 chunk 1329 optimal weight: 4.9990 chunk 1077 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 795 optimal weight: 0.6980 chunk 1398 optimal weight: 1.9990 chunk 393 optimal weight: 9.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1244 GLN B1862 GLN B2096 GLN B2128 GLN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3766 HIS B3767 ASN B4004 GLN ** B4196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1244 GLN E1640 HIS E1862 GLN E2096 GLN E2108 GLN E2128 GLN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3766 HIS E3767 ASN E4029 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1244 GLN H1640 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2128 GLN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3766 HIS H3767 ASN H4029 ASN ** H4196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 399 GLN K1244 GLN K1862 GLN K2128 GLN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3766 HIS K3767 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 113972 Z= 0.204 Angle : 0.562 9.368 155608 Z= 0.279 Chirality : 0.038 0.187 18776 Planarity : 0.004 0.074 20052 Dihedral : 3.862 19.406 16964 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.02 % Allowed : 1.60 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.07), residues: 14452 helix: 1.95 (0.06), residues: 7196 sheet: -0.83 (0.13), residues: 1360 loop : -1.40 (0.08), residues: 5896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 515 HIS 0.007 0.001 HIS B4976 PHE 0.032 0.002 PHE B2013 TYR 0.018 0.002 TYR K1946 ARG 0.007 0.001 ARG K5027 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2316 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2314 time to evaluate : 8.831 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: B 15 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6544 (mtm180) REVERT: B 18 ASP cc_start: 0.7639 (m-30) cc_final: 0.7211 (m-30) REVERT: B 167 ASP cc_start: 0.8908 (m-30) cc_final: 0.8376 (p0) REVERT: B 418 LEU cc_start: 0.8605 (tt) cc_final: 0.8350 (tp) REVERT: B 467 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8129 (mmmt) REVERT: B 573 GLU cc_start: 0.8630 (mp0) cc_final: 0.8030 (pt0) REVERT: B 710 ASP cc_start: 0.8119 (m-30) cc_final: 0.7826 (m-30) REVERT: B 735 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6904 (mm110) REVERT: B 799 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6806 (mp0) REVERT: B 800 PHE cc_start: 0.7539 (m-80) cc_final: 0.6810 (m-80) REVERT: B 847 SER cc_start: 0.7525 (t) cc_final: 0.7264 (p) REVERT: B 1089 TYR cc_start: 0.8201 (t80) cc_final: 0.7721 (t80) REVERT: B 1100 MET cc_start: 0.8332 (ptp) cc_final: 0.7851 (ptt) REVERT: B 1141 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7378 (ptp-170) REVERT: B 1152 MET cc_start: 0.7766 (mpp) cc_final: 0.7246 (mpp) REVERT: B 1245 PHE cc_start: 0.9049 (m-80) cc_final: 0.8372 (m-80) REVERT: B 1293 LEU cc_start: 0.8422 (mt) cc_final: 0.8129 (mp) REVERT: B 1444 GLU cc_start: 0.7545 (mp0) cc_final: 0.7016 (mp0) REVERT: B 1563 GLN cc_start: 0.7443 (mt0) cc_final: 0.7242 (mt0) REVERT: B 1584 ARG cc_start: 0.5921 (tpp-160) cc_final: 0.4837 (tpp-160) REVERT: B 1601 MET cc_start: 0.8375 (tpp) cc_final: 0.7331 (mtm) REVERT: B 1648 MET cc_start: 0.7679 (ttm) cc_final: 0.7438 (ttp) REVERT: B 1703 LEU cc_start: 0.8918 (tp) cc_final: 0.8376 (mp) REVERT: B 1721 GLU cc_start: 0.8498 (tt0) cc_final: 0.8137 (tp30) REVERT: B 1809 ARG cc_start: 0.7853 (ptt180) cc_final: 0.7268 (ptt-90) REVERT: B 2009 MET cc_start: 0.7174 (ttm) cc_final: 0.6493 (tpp) REVERT: B 2171 MET cc_start: 0.7842 (tpp) cc_final: 0.6554 (tpt) REVERT: B 2212 MET cc_start: 0.7700 (tpp) cc_final: 0.7354 (tpp) REVERT: B 2239 TYR cc_start: 0.8164 (m-80) cc_final: 0.7904 (m-80) REVERT: B 2292 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7857 (mm-40) REVERT: B 2319 TYR cc_start: 0.7816 (m-80) cc_final: 0.7424 (m-10) REVERT: B 2616 ARG cc_start: 0.7033 (mtp-110) cc_final: 0.5942 (mtm180) REVERT: B 3438 MET cc_start: 0.6697 (mmp) cc_final: 0.6300 (mmp) REVERT: B 3664 SER cc_start: 0.8943 (m) cc_final: 0.8551 (t) REVERT: B 3806 ASP cc_start: 0.7124 (p0) cc_final: 0.5509 (m-30) REVERT: B 4013 ASP cc_start: 0.8371 (m-30) cc_final: 0.8125 (m-30) REVERT: B 4029 ASN cc_start: 0.7392 (t0) cc_final: 0.7170 (t0) REVERT: B 4059 MET cc_start: 0.5450 (mtt) cc_final: 0.5003 (mtt) REVERT: B 4179 MET cc_start: 0.8399 (tmm) cc_final: 0.7187 (tmm) REVERT: B 4187 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7271 (mtt-85) REVERT: B 4796 MET cc_start: 0.7881 (mmt) cc_final: 0.7435 (tpp) REVERT: B 4802 TYR cc_start: 0.6708 (t80) cc_final: 0.6348 (t80) REVERT: B 4822 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7775 (tpp80) REVERT: C 1 MET cc_start: 0.7083 (mmm) cc_final: 0.6839 (mtp) REVERT: E 15 ARG cc_start: 0.6902 (mtt180) cc_final: 0.6437 (mtm180) REVERT: E 18 ASP cc_start: 0.7561 (m-30) cc_final: 0.7159 (m-30) REVERT: E 167 ASP cc_start: 0.8878 (m-30) cc_final: 0.8407 (p0) REVERT: E 248 GLU cc_start: 0.8005 (pt0) cc_final: 0.7795 (pt0) REVERT: E 418 LEU cc_start: 0.8565 (tt) cc_final: 0.8314 (tp) REVERT: E 467 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8128 (mmmt) REVERT: E 573 GLU cc_start: 0.8621 (mp0) cc_final: 0.7998 (pt0) REVERT: E 710 ASP cc_start: 0.8104 (m-30) cc_final: 0.7817 (m-30) REVERT: E 735 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6915 (mm110) REVERT: E 847 SER cc_start: 0.7533 (t) cc_final: 0.7274 (p) REVERT: E 1089 TYR cc_start: 0.8197 (t80) cc_final: 0.7799 (t80) REVERT: E 1100 MET cc_start: 0.8333 (ptp) cc_final: 0.7838 (ptt) REVERT: E 1141 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7362 (ptp-170) REVERT: E 1152 MET cc_start: 0.7611 (mpp) cc_final: 0.7293 (mpp) REVERT: E 1245 PHE cc_start: 0.9054 (m-80) cc_final: 0.8375 (m-80) REVERT: E 1293 LEU cc_start: 0.8429 (mt) cc_final: 0.8141 (mp) REVERT: E 1444 GLU cc_start: 0.7501 (mp0) cc_final: 0.6971 (mp0) REVERT: E 1584 ARG cc_start: 0.5946 (tpp-160) cc_final: 0.4857 (tpp-160) REVERT: E 1601 MET cc_start: 0.8394 (tpp) cc_final: 0.7377 (mtm) REVERT: E 1648 MET cc_start: 0.7693 (ttm) cc_final: 0.7436 (ttp) REVERT: E 1703 LEU cc_start: 0.8905 (tp) cc_final: 0.8353 (mp) REVERT: E 1809 ARG cc_start: 0.7776 (ptt180) cc_final: 0.7200 (ptt-90) REVERT: E 2009 MET cc_start: 0.7163 (ttm) cc_final: 0.6486 (tpp) REVERT: E 2157 LEU cc_start: 0.8732 (mp) cc_final: 0.8529 (mt) REVERT: E 2171 MET cc_start: 0.7845 (tpp) cc_final: 0.6552 (tpt) REVERT: E 2212 MET cc_start: 0.7703 (tpp) cc_final: 0.7354 (tpp) REVERT: E 2239 TYR cc_start: 0.8164 (m-80) cc_final: 0.7913 (m-80) REVERT: E 2319 TYR cc_start: 0.7818 (m-80) cc_final: 0.7417 (m-10) REVERT: E 2616 ARG cc_start: 0.7027 (mtp-110) cc_final: 0.5931 (mtm180) REVERT: E 3438 MET cc_start: 0.6688 (mmp) cc_final: 0.6292 (mmp) REVERT: E 3664 SER cc_start: 0.8951 (m) cc_final: 0.8599 (t) REVERT: E 3725 MET cc_start: 0.7071 (mtm) cc_final: 0.6422 (mtm) REVERT: E 3727 LYS cc_start: 0.8637 (mttm) cc_final: 0.8365 (ttmm) REVERT: E 3806 ASP cc_start: 0.7069 (p0) cc_final: 0.5487 (m-30) REVERT: E 3940 GLU cc_start: 0.8059 (tp30) cc_final: 0.7845 (tp30) REVERT: E 4013 ASP cc_start: 0.8367 (m-30) cc_final: 0.8146 (m-30) REVERT: E 4034 MET cc_start: 0.5792 (mtp) cc_final: 0.4937 (mmt) REVERT: E 4059 MET cc_start: 0.5312 (mtt) cc_final: 0.5057 (mtt) REVERT: E 4179 MET cc_start: 0.8401 (tmm) cc_final: 0.7188 (tmm) REVERT: E 4187 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7439 (mtt-85) REVERT: E 4796 MET cc_start: 0.7877 (mmt) cc_final: 0.7436 (tpp) REVERT: E 4802 TYR cc_start: 0.6699 (t80) cc_final: 0.6339 (t80) REVERT: E 4822 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7776 (tpp80) REVERT: E 4980 GLU cc_start: 0.7107 (pm20) cc_final: 0.6837 (pm20) REVERT: F 1 MET cc_start: 0.7092 (mmm) cc_final: 0.6852 (mtp) REVERT: H 15 ARG cc_start: 0.6916 (mtt180) cc_final: 0.6444 (mtm180) REVERT: H 18 ASP cc_start: 0.7563 (m-30) cc_final: 0.7166 (m-30) REVERT: H 248 GLU cc_start: 0.8024 (pt0) cc_final: 0.7802 (pt0) REVERT: H 418 LEU cc_start: 0.8576 (tt) cc_final: 0.8305 (tp) REVERT: H 467 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8127 (mmmt) REVERT: H 573 GLU cc_start: 0.8589 (mp0) cc_final: 0.8011 (pt0) REVERT: H 710 ASP cc_start: 0.8102 (m-30) cc_final: 0.7820 (m-30) REVERT: H 735 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6919 (mm110) REVERT: H 847 SER cc_start: 0.7533 (t) cc_final: 0.7271 (p) REVERT: H 1089 TYR cc_start: 0.8171 (t80) cc_final: 0.7677 (t80) REVERT: H 1100 MET cc_start: 0.8322 (ptp) cc_final: 0.7835 (ptt) REVERT: H 1141 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7353 (ptp-170) REVERT: H 1152 MET cc_start: 0.7199 (mpp) cc_final: 0.6686 (mpp) REVERT: H 1245 PHE cc_start: 0.9054 (m-80) cc_final: 0.8383 (m-80) REVERT: H 1293 LEU cc_start: 0.8430 (mt) cc_final: 0.8143 (mp) REVERT: H 1444 GLU cc_start: 0.7506 (mp0) cc_final: 0.6970 (mp0) REVERT: H 1584 ARG cc_start: 0.5948 (tpp-160) cc_final: 0.4858 (tpp-160) REVERT: H 1601 MET cc_start: 0.8384 (tpp) cc_final: 0.7369 (mtm) REVERT: H 1648 MET cc_start: 0.7684 (ttm) cc_final: 0.7429 (ttp) REVERT: H 1703 LEU cc_start: 0.8914 (tp) cc_final: 0.8335 (mp) REVERT: H 1809 ARG cc_start: 0.7778 (ptt180) cc_final: 0.7195 (ptt-90) REVERT: H 2009 MET cc_start: 0.7176 (ttm) cc_final: 0.6501 (tpp) REVERT: H 2157 LEU cc_start: 0.8726 (mp) cc_final: 0.8523 (mt) REVERT: H 2171 MET cc_start: 0.7839 (tpp) cc_final: 0.6543 (tpt) REVERT: H 2212 MET cc_start: 0.7694 (tpp) cc_final: 0.7311 (tpp) REVERT: H 2239 TYR cc_start: 0.8145 (m-80) cc_final: 0.7920 (m-80) REVERT: H 2247 ASN cc_start: 0.8884 (m-40) cc_final: 0.8667 (m110) REVERT: H 2275 ASP cc_start: 0.8036 (t0) cc_final: 0.7799 (t0) REVERT: H 2292 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7859 (mm-40) REVERT: H 2319 TYR cc_start: 0.7809 (m-80) cc_final: 0.7405 (m-10) REVERT: H 2616 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.5880 (mtm180) REVERT: H 3438 MET cc_start: 0.6696 (mmp) cc_final: 0.6302 (mmp) REVERT: H 3664 SER cc_start: 0.8957 (m) cc_final: 0.8605 (t) REVERT: H 3725 MET cc_start: 0.6967 (mtm) cc_final: 0.6287 (mtm) REVERT: H 3806 ASP cc_start: 0.7137 (p0) cc_final: 0.5531 (m-30) REVERT: H 4013 ASP cc_start: 0.8375 (m-30) cc_final: 0.8125 (m-30) REVERT: H 4034 MET cc_start: 0.5815 (mtp) cc_final: 0.4942 (mmt) REVERT: H 4179 MET cc_start: 0.8416 (tmm) cc_final: 0.7205 (tmm) REVERT: H 4187 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7433 (mtt-85) REVERT: H 4796 MET cc_start: 0.7878 (mmt) cc_final: 0.7436 (tpp) REVERT: H 4802 TYR cc_start: 0.6707 (t80) cc_final: 0.6344 (t80) REVERT: H 4822 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7779 (tpp80) REVERT: H 4980 GLU cc_start: 0.7233 (pm20) cc_final: 0.7011 (pm20) REVERT: I 1 MET cc_start: 0.7056 (mmm) cc_final: 0.6531 (mtt) REVERT: K 15 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6469 (mtm-85) REVERT: K 18 ASP cc_start: 0.7570 (m-30) cc_final: 0.7179 (m-30) REVERT: K 248 GLU cc_start: 0.8012 (pt0) cc_final: 0.7781 (pt0) REVERT: K 418 LEU cc_start: 0.8606 (tt) cc_final: 0.8347 (tp) REVERT: K 467 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8119 (mmmt) REVERT: K 573 GLU cc_start: 0.8662 (mp0) cc_final: 0.8021 (pt0) REVERT: K 710 ASP cc_start: 0.8111 (m-30) cc_final: 0.7825 (m-30) REVERT: K 735 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6915 (mm110) REVERT: K 847 SER cc_start: 0.7536 (t) cc_final: 0.7283 (p) REVERT: K 1089 TYR cc_start: 0.8198 (t80) cc_final: 0.7807 (t80) REVERT: K 1100 MET cc_start: 0.8328 (ptp) cc_final: 0.7838 (ptt) REVERT: K 1141 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7344 (ptp-170) REVERT: K 1152 MET cc_start: 0.7610 (mpp) cc_final: 0.7285 (mpp) REVERT: K 1245 PHE cc_start: 0.9052 (m-80) cc_final: 0.8393 (m-80) REVERT: K 1293 LEU cc_start: 0.8449 (mt) cc_final: 0.8159 (mp) REVERT: K 1444 GLU cc_start: 0.7502 (mp0) cc_final: 0.6978 (mp0) REVERT: K 1584 ARG cc_start: 0.5950 (tpp-160) cc_final: 0.4873 (tpp-160) REVERT: K 1601 MET cc_start: 0.8384 (tpp) cc_final: 0.7395 (mtm) REVERT: K 1703 LEU cc_start: 0.8915 (tp) cc_final: 0.8353 (mp) REVERT: K 1809 ARG cc_start: 0.7859 (ptt180) cc_final: 0.7253 (ptt-90) REVERT: K 2000 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7364 (mtp85) REVERT: K 2009 MET cc_start: 0.7171 (ttm) cc_final: 0.6493 (tpp) REVERT: K 2171 MET cc_start: 0.7914 (tpp) cc_final: 0.6644 (tpt) REVERT: K 2209 MET cc_start: 0.7398 (ttp) cc_final: 0.7076 (ttm) REVERT: K 2212 MET cc_start: 0.7655 (tpp) cc_final: 0.7354 (tpp) REVERT: K 2239 TYR cc_start: 0.8124 (m-80) cc_final: 0.7906 (m-80) REVERT: K 2275 ASP cc_start: 0.8030 (t0) cc_final: 0.7782 (t0) REVERT: K 2319 TYR cc_start: 0.7813 (m-80) cc_final: 0.7376 (m-10) REVERT: K 2616 ARG cc_start: 0.7028 (mtp-110) cc_final: 0.5938 (mtm180) REVERT: K 3438 MET cc_start: 0.6707 (mmp) cc_final: 0.6309 (mmp) REVERT: K 3664 SER cc_start: 0.8965 (m) cc_final: 0.8607 (t) REVERT: K 3725 MET cc_start: 0.6940 (mtm) cc_final: 0.6302 (mtm) REVERT: K 3727 LYS cc_start: 0.8659 (mttm) cc_final: 0.8399 (ttmm) REVERT: K 3772 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8252 (mm-30) REVERT: K 3806 ASP cc_start: 0.7159 (p0) cc_final: 0.5566 (m-30) REVERT: K 4013 ASP cc_start: 0.8371 (m-30) cc_final: 0.8133 (m-30) REVERT: K 4029 ASN cc_start: 0.7443 (t0) cc_final: 0.7238 (t0) REVERT: K 4032 ASN cc_start: 0.6444 (m-40) cc_final: 0.6027 (t0) REVERT: K 4034 MET cc_start: 0.5397 (mtt) cc_final: 0.4660 (mmt) REVERT: K 4179 MET cc_start: 0.8415 (tmm) cc_final: 0.7481 (tmm) REVERT: K 4187 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7396 (mtt-85) REVERT: K 4796 MET cc_start: 0.7887 (mmt) cc_final: 0.7440 (tpp) REVERT: K 4802 TYR cc_start: 0.6709 (t80) cc_final: 0.6341 (t80) REVERT: K 4822 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7775 (tpp80) outliers start: 2 outliers final: 2 residues processed: 2314 average time/residue: 0.9650 time to fit residues: 4042.6655 Evaluate side-chains 2046 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2044 time to evaluate : 8.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 524 optimal weight: 0.4980 chunk 1403 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 914 optimal weight: 20.0000 chunk 384 optimal weight: 5.9990 chunk 1559 optimal weight: 3.9990 chunk 1294 optimal weight: 10.0000 chunk 722 optimal weight: 3.9990 chunk 129 optimal weight: 0.0270 chunk 515 optimal weight: 7.9990 chunk 818 optimal weight: 4.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN B1776 HIS B1862 GLN B1950 GLN B2096 GLN B2108 GLN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 ASN E 113 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1231 GLN E1776 HIS E1862 GLN E1950 GLN E2096 GLN ** E2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3767 ASN ** E3804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4029 ASN H 113 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1231 GLN H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3695 HIS H3696 GLN H3767 ASN H4004 GLN H4029 ASN K 113 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1231 GLN K1776 HIS K1862 GLN K1950 GLN K2108 GLN K2247 ASN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3767 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 113972 Z= 0.267 Angle : 0.603 10.858 155608 Z= 0.302 Chirality : 0.039 0.212 18776 Planarity : 0.004 0.069 20052 Dihedral : 3.943 20.006 16964 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.02 % Allowed : 1.64 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.07), residues: 14452 helix: 1.96 (0.06), residues: 7204 sheet: -0.86 (0.14), residues: 1356 loop : -1.42 (0.08), residues: 5892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K1143 HIS 0.007 0.001 HIS H4884 PHE 0.020 0.002 PHE K2013 TYR 0.028 0.002 TYR K4713 ARG 0.007 0.001 ARG E5027 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2287 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2285 time to evaluate : 8.990 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: A 31 GLN cc_start: 0.6438 (tt0) cc_final: 0.6177 (tt0) REVERT: A 96 THR cc_start: 0.8884 (p) cc_final: 0.8666 (p) REVERT: B 15 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6550 (mtm-85) REVERT: B 18 ASP cc_start: 0.7677 (m-30) cc_final: 0.7294 (m-30) REVERT: B 134 ASP cc_start: 0.7845 (m-30) cc_final: 0.7573 (m-30) REVERT: B 167 ASP cc_start: 0.8873 (m-30) cc_final: 0.8380 (p0) REVERT: B 418 LEU cc_start: 0.8588 (tt) cc_final: 0.8340 (tp) REVERT: B 710 ASP cc_start: 0.8279 (m-30) cc_final: 0.7994 (m-30) REVERT: B 735 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7079 (mm110) REVERT: B 799 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6725 (mp0) REVERT: B 847 SER cc_start: 0.7554 (t) cc_final: 0.7301 (p) REVERT: B 1089 TYR cc_start: 0.8163 (t80) cc_final: 0.7695 (t80) REVERT: B 1100 MET cc_start: 0.8204 (ptp) cc_final: 0.7922 (ptt) REVERT: B 1141 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7418 (ptp-170) REVERT: B 1152 MET cc_start: 0.7848 (mpp) cc_final: 0.7295 (mpp) REVERT: B 1245 PHE cc_start: 0.9094 (m-80) cc_final: 0.8369 (m-80) REVERT: B 1293 LEU cc_start: 0.8635 (mt) cc_final: 0.8360 (mt) REVERT: B 1444 GLU cc_start: 0.7583 (mp0) cc_final: 0.7050 (mp0) REVERT: B 1601 MET cc_start: 0.8294 (tpp) cc_final: 0.7135 (mtm) REVERT: B 1854 ILE cc_start: 0.9064 (mm) cc_final: 0.8849 (mm) REVERT: B 1930 MET cc_start: 0.7994 (ttt) cc_final: 0.7696 (ttt) REVERT: B 2009 MET cc_start: 0.7428 (ttm) cc_final: 0.6598 (tpp) REVERT: B 2013 PHE cc_start: 0.8387 (t80) cc_final: 0.7965 (t80) REVERT: B 2171 MET cc_start: 0.7910 (tpp) cc_final: 0.7588 (mmt) REVERT: B 2212 MET cc_start: 0.7519 (tpp) cc_final: 0.6898 (tpt) REVERT: B 2239 TYR cc_start: 0.8175 (m-80) cc_final: 0.7915 (m-80) REVERT: B 2251 MET cc_start: 0.9469 (mmm) cc_final: 0.9031 (tpt) REVERT: B 2292 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7770 (mm-40) REVERT: B 2319 TYR cc_start: 0.7859 (m-80) cc_final: 0.7455 (m-10) REVERT: B 2616 ARG cc_start: 0.7072 (mtp-110) cc_final: 0.5856 (mtt180) REVERT: B 3438 MET cc_start: 0.6713 (mmp) cc_final: 0.6343 (mmp) REVERT: B 3664 SER cc_start: 0.8976 (m) cc_final: 0.8651 (t) REVERT: B 3669 MET cc_start: 0.7555 (ttt) cc_final: 0.6365 (ttp) REVERT: B 3725 MET cc_start: 0.7111 (mtm) cc_final: 0.6457 (mtm) REVERT: B 3806 ASP cc_start: 0.7185 (p0) cc_final: 0.5422 (m-30) REVERT: B 4013 ASP cc_start: 0.8384 (m-30) cc_final: 0.8148 (m-30) REVERT: B 4029 ASN cc_start: 0.7452 (t0) cc_final: 0.7219 (t0) REVERT: B 4034 MET cc_start: 0.5952 (mtt) cc_final: 0.5359 (mmt) REVERT: B 4179 MET cc_start: 0.8441 (tmm) cc_final: 0.7393 (tmm) REVERT: B 4187 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7352 (mtt-85) REVERT: B 4555 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7704 (mtt180) REVERT: B 4802 TYR cc_start: 0.6838 (t80) cc_final: 0.6451 (t80) REVERT: B 4837 MET cc_start: 0.9250 (mmm) cc_final: 0.8954 (mmp) REVERT: D 31 GLN cc_start: 0.6440 (tt0) cc_final: 0.6191 (tt0) REVERT: D 96 THR cc_start: 0.8885 (p) cc_final: 0.8683 (p) REVERT: E 15 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6524 (mtm180) REVERT: E 18 ASP cc_start: 0.7692 (m-30) cc_final: 0.7252 (m-30) REVERT: E 134 ASP cc_start: 0.7769 (m-30) cc_final: 0.7522 (m-30) REVERT: E 167 ASP cc_start: 0.8873 (m-30) cc_final: 0.8409 (p0) REVERT: E 403 MET cc_start: 0.8624 (mtm) cc_final: 0.8317 (ttm) REVERT: E 418 LEU cc_start: 0.8549 (tt) cc_final: 0.8310 (tp) REVERT: E 467 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8147 (mmmt) REVERT: E 710 ASP cc_start: 0.8264 (m-30) cc_final: 0.7982 (m-30) REVERT: E 735 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7066 (mm110) REVERT: E 847 SER cc_start: 0.7559 (t) cc_final: 0.7306 (p) REVERT: E 1089 TYR cc_start: 0.8149 (t80) cc_final: 0.7795 (t80) REVERT: E 1100 MET cc_start: 0.8227 (ptp) cc_final: 0.7955 (ptt) REVERT: E 1141 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7422 (ptp-170) REVERT: E 1152 MET cc_start: 0.7730 (mpp) cc_final: 0.7312 (mpp) REVERT: E 1245 PHE cc_start: 0.9113 (m-80) cc_final: 0.8422 (m-80) REVERT: E 1293 LEU cc_start: 0.8645 (mt) cc_final: 0.8372 (mt) REVERT: E 1444 GLU cc_start: 0.7549 (mp0) cc_final: 0.7003 (mp0) REVERT: E 1601 MET cc_start: 0.8356 (tpp) cc_final: 0.7264 (mtm) REVERT: E 1648 MET cc_start: 0.7750 (ttm) cc_final: 0.7544 (ttp) REVERT: E 1703 LEU cc_start: 0.8995 (tp) cc_final: 0.8496 (mp) REVERT: E 1854 ILE cc_start: 0.9006 (mm) cc_final: 0.8729 (mm) REVERT: E 2009 MET cc_start: 0.7416 (ttm) cc_final: 0.6595 (tpp) REVERT: E 2013 PHE cc_start: 0.8384 (t80) cc_final: 0.7953 (t80) REVERT: E 2171 MET cc_start: 0.7912 (tpp) cc_final: 0.7580 (mmt) REVERT: E 2212 MET cc_start: 0.7569 (tpp) cc_final: 0.7090 (tpt) REVERT: E 2239 TYR cc_start: 0.8183 (m-80) cc_final: 0.7918 (m-80) REVERT: E 2251 MET cc_start: 0.9464 (mmm) cc_final: 0.9021 (tpt) REVERT: E 2292 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7772 (mm-40) REVERT: E 2319 TYR cc_start: 0.7860 (m-80) cc_final: 0.7445 (m-10) REVERT: E 2616 ARG cc_start: 0.7083 (mtp-110) cc_final: 0.5991 (mtm180) REVERT: E 3438 MET cc_start: 0.6705 (mmp) cc_final: 0.6334 (mmp) REVERT: E 3664 SER cc_start: 0.9063 (m) cc_final: 0.8711 (t) REVERT: E 3725 MET cc_start: 0.7003 (mtm) cc_final: 0.6407 (mtm) REVERT: E 3806 ASP cc_start: 0.7250 (p0) cc_final: 0.5583 (m-30) REVERT: E 4013 ASP cc_start: 0.8386 (m-30) cc_final: 0.8162 (m-30) REVERT: E 4034 MET cc_start: 0.5920 (mtp) cc_final: 0.4999 (mmt) REVERT: E 4179 MET cc_start: 0.8450 (tmm) cc_final: 0.7408 (tmm) REVERT: E 4187 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: E 4555 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.7703 (mtt180) REVERT: E 4802 TYR cc_start: 0.6807 (t80) cc_final: 0.6424 (t80) REVERT: E 4837 MET cc_start: 0.9250 (mmm) cc_final: 0.8958 (mmp) REVERT: E 4980 GLU cc_start: 0.7477 (pm20) cc_final: 0.7154 (pm20) REVERT: G 31 GLN cc_start: 0.6441 (tt0) cc_final: 0.6195 (tt0) REVERT: H 15 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6526 (mtm180) REVERT: H 18 ASP cc_start: 0.7705 (m-30) cc_final: 0.7233 (m-30) REVERT: H 134 ASP cc_start: 0.7803 (m-30) cc_final: 0.7561 (m-30) REVERT: H 403 MET cc_start: 0.8630 (mtm) cc_final: 0.8316 (ttm) REVERT: H 418 LEU cc_start: 0.8557 (tt) cc_final: 0.8313 (tp) REVERT: H 467 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8156 (mmmt) REVERT: H 710 ASP cc_start: 0.8261 (m-30) cc_final: 0.7982 (m-30) REVERT: H 735 GLN cc_start: 0.7348 (mm-40) cc_final: 0.7063 (mm110) REVERT: H 847 SER cc_start: 0.7560 (t) cc_final: 0.7306 (p) REVERT: H 1089 TYR cc_start: 0.8188 (t80) cc_final: 0.7760 (t80) REVERT: H 1100 MET cc_start: 0.8201 (ptp) cc_final: 0.7928 (ptt) REVERT: H 1141 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7406 (ptp-170) REVERT: H 1152 MET cc_start: 0.7253 (mpp) cc_final: 0.6829 (mpp) REVERT: H 1245 PHE cc_start: 0.9113 (m-80) cc_final: 0.8391 (m-80) REVERT: H 1293 LEU cc_start: 0.8649 (mt) cc_final: 0.8376 (mt) REVERT: H 1444 GLU cc_start: 0.7547 (mp0) cc_final: 0.7004 (mp0) REVERT: H 1601 MET cc_start: 0.8367 (tpp) cc_final: 0.7290 (mtm) REVERT: H 1648 MET cc_start: 0.7750 (ttm) cc_final: 0.7546 (ttp) REVERT: H 1854 ILE cc_start: 0.8994 (mm) cc_final: 0.8729 (mm) REVERT: H 2009 MET cc_start: 0.7429 (ttm) cc_final: 0.6598 (tpp) REVERT: H 2013 PHE cc_start: 0.8383 (t80) cc_final: 0.7960 (t80) REVERT: H 2171 MET cc_start: 0.7910 (tpp) cc_final: 0.7581 (mmt) REVERT: H 2212 MET cc_start: 0.7554 (tpp) cc_final: 0.6884 (tpt) REVERT: H 2239 TYR cc_start: 0.8198 (m-80) cc_final: 0.7964 (m-80) REVERT: H 2275 ASP cc_start: 0.8008 (t0) cc_final: 0.7796 (t0) REVERT: H 2292 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7784 (mm-40) REVERT: H 2319 TYR cc_start: 0.7853 (m-80) cc_final: 0.7447 (m-10) REVERT: H 2616 ARG cc_start: 0.7065 (mtp-110) cc_final: 0.5934 (mtm180) REVERT: H 3438 MET cc_start: 0.6716 (mmp) cc_final: 0.6349 (mmp) REVERT: H 3664 SER cc_start: 0.9071 (m) cc_final: 0.8725 (t) REVERT: H 3725 MET cc_start: 0.7015 (mtm) cc_final: 0.6405 (mtm) REVERT: H 3806 ASP cc_start: 0.7184 (p0) cc_final: 0.5399 (m-30) REVERT: H 4013 ASP cc_start: 0.8378 (m-30) cc_final: 0.8144 (m-30) REVERT: H 4034 MET cc_start: 0.6031 (mtp) cc_final: 0.5055 (mmt) REVERT: H 4179 MET cc_start: 0.8516 (tmm) cc_final: 0.7377 (tmm) REVERT: H 4187 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7370 (mtt-85) REVERT: H 4555 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7710 (mtt180) REVERT: H 4802 TYR cc_start: 0.6846 (t80) cc_final: 0.6453 (t80) REVERT: H 4822 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7760 (tpp80) REVERT: H 4837 MET cc_start: 0.9253 (mmm) cc_final: 0.8963 (mmp) REVERT: H 4877 MET cc_start: 0.7457 (ttp) cc_final: 0.7163 (ttp) REVERT: H 4980 GLU cc_start: 0.7471 (pm20) cc_final: 0.7160 (pm20) REVERT: J 31 GLN cc_start: 0.6444 (tt0) cc_final: 0.6199 (tt0) REVERT: J 96 THR cc_start: 0.8885 (p) cc_final: 0.8678 (p) REVERT: K 15 ARG cc_start: 0.6855 (mtt180) cc_final: 0.6450 (mtm-85) REVERT: K 18 ASP cc_start: 0.7715 (m-30) cc_final: 0.7270 (m-30) REVERT: K 134 ASP cc_start: 0.7798 (m-30) cc_final: 0.7547 (m-30) REVERT: K 418 LEU cc_start: 0.8565 (tt) cc_final: 0.8345 (tp) REVERT: K 467 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8141 (mmmt) REVERT: K 710 ASP cc_start: 0.8268 (m-30) cc_final: 0.7990 (m-30) REVERT: K 735 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7062 (mm110) REVERT: K 847 SER cc_start: 0.7569 (t) cc_final: 0.7320 (p) REVERT: K 1089 TYR cc_start: 0.8149 (t80) cc_final: 0.7698 (t80) REVERT: K 1100 MET cc_start: 0.8235 (ptp) cc_final: 0.7968 (ptt) REVERT: K 1141 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7404 (ptp-170) REVERT: K 1152 MET cc_start: 0.7724 (mpp) cc_final: 0.7302 (mpp) REVERT: K 1245 PHE cc_start: 0.9112 (m-80) cc_final: 0.8401 (m-80) REVERT: K 1293 LEU cc_start: 0.8666 (mt) cc_final: 0.8397 (mt) REVERT: K 1444 GLU cc_start: 0.7554 (mp0) cc_final: 0.7010 (mp0) REVERT: K 1563 GLN cc_start: 0.7588 (mt0) cc_final: 0.7388 (mt0) REVERT: K 1601 MET cc_start: 0.8358 (tpp) cc_final: 0.7280 (mtm) REVERT: K 1854 ILE cc_start: 0.9009 (mm) cc_final: 0.8734 (mm) REVERT: K 2000 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7396 (mtp85) REVERT: K 2009 MET cc_start: 0.7428 (ttm) cc_final: 0.6588 (tpp) REVERT: K 2013 PHE cc_start: 0.8370 (t80) cc_final: 0.7951 (t80) REVERT: K 2171 MET cc_start: 0.7977 (tpp) cc_final: 0.7664 (mmt) REVERT: K 2212 MET cc_start: 0.7480 (tpp) cc_final: 0.6836 (tpt) REVERT: K 2239 TYR cc_start: 0.8190 (m-80) cc_final: 0.7955 (m-80) REVERT: K 2275 ASP cc_start: 0.7999 (t0) cc_final: 0.7799 (t0) REVERT: K 2292 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7784 (mm-40) REVERT: K 2319 TYR cc_start: 0.7852 (m-80) cc_final: 0.7409 (m-10) REVERT: K 2616 ARG cc_start: 0.7084 (mtp-110) cc_final: 0.5987 (mtm180) REVERT: K 3438 MET cc_start: 0.6729 (mmp) cc_final: 0.6353 (mmp) REVERT: K 3664 SER cc_start: 0.9041 (m) cc_final: 0.8723 (t) REVERT: K 3725 MET cc_start: 0.7008 (mtm) cc_final: 0.6402 (mtm) REVERT: K 3753 MET cc_start: 0.6761 (tpp) cc_final: 0.6239 (tpt) REVERT: K 3804 ASN cc_start: 0.6680 (m-40) cc_final: 0.6465 (m-40) REVERT: K 3806 ASP cc_start: 0.7197 (p0) cc_final: 0.5430 (m-30) REVERT: K 3831 MET cc_start: 0.7982 (mtm) cc_final: 0.7556 (mtp) REVERT: K 4013 ASP cc_start: 0.8386 (m-30) cc_final: 0.8150 (m-30) REVERT: K 4029 ASN cc_start: 0.7526 (t0) cc_final: 0.7297 (t0) REVERT: K 4032 ASN cc_start: 0.6537 (m-40) cc_final: 0.6311 (t0) REVERT: K 4034 MET cc_start: 0.5538 (mtt) cc_final: 0.4875 (mmt) REVERT: K 4179 MET cc_start: 0.8475 (tmm) cc_final: 0.7525 (tmm) REVERT: K 4187 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7402 (mtt-85) REVERT: K 4555 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.7720 (mtt180) REVERT: K 4802 TYR cc_start: 0.6835 (t80) cc_final: 0.6446 (t80) REVERT: K 4837 MET cc_start: 0.9257 (mmm) cc_final: 0.8957 (mmp) REVERT: K 4980 GLU cc_start: 0.7317 (pm20) cc_final: 0.7033 (pm20) REVERT: L 1 MET cc_start: 0.7203 (mtp) cc_final: 0.6877 (mtt) outliers start: 2 outliers final: 0 residues processed: 2285 average time/residue: 0.8583 time to fit residues: 3523.8909 Evaluate side-chains 2008 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2008 time to evaluate : 8.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1503 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 888 optimal weight: 4.9990 chunk 1138 optimal weight: 8.9990 chunk 882 optimal weight: 8.9990 chunk 1312 optimal weight: 20.0000 chunk 870 optimal weight: 0.9990 chunk 1553 optimal weight: 4.9990 chunk 972 optimal weight: 6.9990 chunk 947 optimal weight: 8.9990 chunk 717 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1761 HIS B1776 HIS B1862 GLN B2096 GLN ** B2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2128 GLN B2247 ASN B2261 ASN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 ASN ** B3776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4218 ASN ** B4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS E 681 HIS E1683 HIS E1761 HIS E1776 HIS E1862 GLN E2096 GLN ** E2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2128 GLN E2247 ASN E2261 ASN E2521 HIS ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3767 ASN E4004 GLN E4029 ASN E4218 ASN ** E4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS H 681 HIS H1611 HIS H1683 HIS H1761 HIS H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2128 GLN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3663 HIS H3696 GLN H3767 ASN ** H4029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4218 ASN ** H4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 HIS K 399 GLN K 681 HIS K1611 HIS K1761 HIS K1776 HIS K1862 GLN ** K2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2128 GLN K2247 ASN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3663 HIS K3767 ASN ** K3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4004 GLN K4218 ASN ** K4648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 113972 Z= 0.408 Angle : 0.738 12.261 155608 Z= 0.375 Chirality : 0.043 0.214 18776 Planarity : 0.005 0.088 20052 Dihedral : 4.503 22.929 16964 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.01 % Allowed : 1.37 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.07), residues: 14452 helix: 1.49 (0.06), residues: 7188 sheet: -1.02 (0.13), residues: 1376 loop : -1.54 (0.08), residues: 5888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 515 HIS 0.013 0.002 HIS B4884 PHE 0.047 0.003 PHE H5020 TYR 0.049 0.003 TYR K4986 ARG 0.009 0.001 ARG B1290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2247 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2246 time to evaluate : 8.885 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: A 31 GLN cc_start: 0.6537 (tt0) cc_final: 0.6275 (tt0) REVERT: B 134 ASP cc_start: 0.7899 (m-30) cc_final: 0.7654 (m-30) REVERT: B 167 ASP cc_start: 0.9016 (m-30) cc_final: 0.8803 (m-30) REVERT: B 255 HIS cc_start: 0.7176 (m90) cc_final: 0.6941 (m-70) REVERT: B 404 ILE cc_start: 0.9278 (mt) cc_final: 0.9033 (mt) REVERT: B 418 LEU cc_start: 0.8589 (tt) cc_final: 0.8337 (tp) REVERT: B 710 ASP cc_start: 0.8260 (m-30) cc_final: 0.7991 (m-30) REVERT: B 735 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6995 (mm110) REVERT: B 799 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6629 (mp0) REVERT: B 801 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7321 (mmtt) REVERT: B 847 SER cc_start: 0.7643 (t) cc_final: 0.7350 (p) REVERT: B 1089 TYR cc_start: 0.8216 (t80) cc_final: 0.7940 (t80) REVERT: B 1141 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7378 (ptp-170) REVERT: B 1152 MET cc_start: 0.7799 (mpp) cc_final: 0.7390 (mpp) REVERT: B 1293 LEU cc_start: 0.8369 (mt) cc_final: 0.8022 (mp) REVERT: B 1444 GLU cc_start: 0.7702 (mp0) cc_final: 0.7093 (mp0) REVERT: B 1446 SER cc_start: 0.8576 (p) cc_final: 0.8201 (m) REVERT: B 1563 GLN cc_start: 0.7350 (mt0) cc_final: 0.7103 (mt0) REVERT: B 1600 LEU cc_start: 0.7939 (tp) cc_final: 0.7718 (tp) REVERT: B 1601 MET cc_start: 0.8367 (tpp) cc_final: 0.7330 (mtm) REVERT: B 1761 HIS cc_start: 0.8505 (m-70) cc_final: 0.8108 (m-70) REVERT: B 1854 ILE cc_start: 0.9159 (mm) cc_final: 0.8874 (mm) REVERT: B 2009 MET cc_start: 0.7505 (ttm) cc_final: 0.6781 (tpp) REVERT: B 2146 SER cc_start: 0.7605 (p) cc_final: 0.7290 (t) REVERT: B 2171 MET cc_start: 0.8003 (tpp) cc_final: 0.7737 (tpt) REVERT: B 2204 MET cc_start: 0.8434 (mtp) cc_final: 0.8149 (mtp) REVERT: B 2212 MET cc_start: 0.7620 (tpp) cc_final: 0.6927 (tpt) REVERT: B 2239 TYR cc_start: 0.8269 (m-80) cc_final: 0.7914 (m-80) REVERT: B 2251 MET cc_start: 0.9204 (tpt) cc_final: 0.8629 (tpt) REVERT: B 2292 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7770 (mm-40) REVERT: B 2319 TYR cc_start: 0.8082 (m-80) cc_final: 0.7563 (m-10) REVERT: B 2616 ARG cc_start: 0.7036 (mtp-110) cc_final: 0.5902 (mtt180) REVERT: B 3664 SER cc_start: 0.9131 (m) cc_final: 0.8819 (t) REVERT: B 3725 MET cc_start: 0.7182 (mtm) cc_final: 0.6414 (mtm) REVERT: B 3806 ASP cc_start: 0.7223 (p0) cc_final: 0.5608 (m-30) REVERT: B 4013 ASP cc_start: 0.8418 (m-30) cc_final: 0.8169 (m-30) REVERT: B 4034 MET cc_start: 0.6017 (mtt) cc_final: 0.5392 (mmm) REVERT: B 4179 MET cc_start: 0.8525 (tmm) cc_final: 0.7434 (tmm) REVERT: B 4187 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7438 (mtt-85) REVERT: B 4555 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7577 (mtt180) REVERT: B 4802 TYR cc_start: 0.6982 (t80) cc_final: 0.6614 (t80) REVERT: B 4837 MET cc_start: 0.9242 (mmm) cc_final: 0.9002 (mmp) REVERT: B 4980 GLU cc_start: 0.6922 (mp0) cc_final: 0.6332 (mp0) REVERT: D 31 GLN cc_start: 0.6539 (tt0) cc_final: 0.6302 (tt0) REVERT: E 134 ASP cc_start: 0.7870 (m-30) cc_final: 0.7647 (m-30) REVERT: E 167 ASP cc_start: 0.9099 (m-30) cc_final: 0.8863 (m-30) REVERT: E 403 MET cc_start: 0.8649 (mtm) cc_final: 0.8174 (ttm) REVERT: E 418 LEU cc_start: 0.8577 (tt) cc_final: 0.8337 (tp) REVERT: E 710 ASP cc_start: 0.8233 (m-30) cc_final: 0.7970 (m-30) REVERT: E 735 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6912 (mm110) REVERT: E 823 LEU cc_start: 0.6707 (mm) cc_final: 0.6504 (mm) REVERT: E 847 SER cc_start: 0.7648 (t) cc_final: 0.7358 (p) REVERT: E 1089 TYR cc_start: 0.8254 (t80) cc_final: 0.7858 (t80) REVERT: E 1141 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7394 (ptp-170) REVERT: E 1152 MET cc_start: 0.7696 (mpp) cc_final: 0.7222 (mpp) REVERT: E 1293 LEU cc_start: 0.8391 (mt) cc_final: 0.8114 (mt) REVERT: E 1444 GLU cc_start: 0.7676 (mp0) cc_final: 0.7104 (mp0) REVERT: E 1601 MET cc_start: 0.8361 (tpp) cc_final: 0.7601 (mtm) REVERT: E 1671 ARG cc_start: 0.7412 (mtm110) cc_final: 0.5564 (ttt-90) REVERT: E 1761 HIS cc_start: 0.8514 (m-70) cc_final: 0.8098 (m-70) REVERT: E 1854 ILE cc_start: 0.9050 (mm) cc_final: 0.8823 (mm) REVERT: E 1930 MET cc_start: 0.7906 (ttt) cc_final: 0.7652 (ttt) REVERT: E 2009 MET cc_start: 0.7495 (ttm) cc_final: 0.6769 (tpp) REVERT: E 2013 PHE cc_start: 0.8557 (t80) cc_final: 0.8349 (t80) REVERT: E 2146 SER cc_start: 0.7567 (p) cc_final: 0.7231 (t) REVERT: E 2171 MET cc_start: 0.8059 (tpp) cc_final: 0.7741 (tpt) REVERT: E 2204 MET cc_start: 0.8398 (mtp) cc_final: 0.8110 (mtp) REVERT: E 2212 MET cc_start: 0.7556 (tpp) cc_final: 0.6929 (tpt) REVERT: E 2239 TYR cc_start: 0.8246 (m-80) cc_final: 0.7905 (m-80) REVERT: E 2251 MET cc_start: 0.9200 (tpt) cc_final: 0.8629 (tpt) REVERT: E 2292 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7784 (mm-40) REVERT: E 2319 TYR cc_start: 0.8082 (m-80) cc_final: 0.7555 (m-10) REVERT: E 2441 MET cc_start: 0.6269 (ttt) cc_final: 0.6049 (mmm) REVERT: E 2616 ARG cc_start: 0.7032 (mtp-110) cc_final: 0.5900 (mtt180) REVERT: E 3664 SER cc_start: 0.9178 (m) cc_final: 0.8849 (t) REVERT: E 3725 MET cc_start: 0.7107 (mtm) cc_final: 0.6421 (mtm) REVERT: E 3772 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8174 (mm-30) REVERT: E 3806 ASP cc_start: 0.7234 (p0) cc_final: 0.5622 (m-30) REVERT: E 4013 ASP cc_start: 0.8417 (m-30) cc_final: 0.8174 (m-30) REVERT: E 4034 MET cc_start: 0.6066 (mtp) cc_final: 0.5115 (mmt) REVERT: E 4136 PHE cc_start: 0.8352 (t80) cc_final: 0.7889 (t80) REVERT: E 4179 MET cc_start: 0.8460 (tmm) cc_final: 0.7393 (tmm) REVERT: E 4187 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7476 (mtt-85) REVERT: E 4191 GLU cc_start: 0.8422 (tt0) cc_final: 0.7931 (tt0) REVERT: E 4555 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7574 (mtt180) REVERT: E 4802 TYR cc_start: 0.6971 (t80) cc_final: 0.6555 (t80) REVERT: E 4837 MET cc_start: 0.9236 (mmm) cc_final: 0.9002 (mmp) REVERT: E 4980 GLU cc_start: 0.7649 (pm20) cc_final: 0.7308 (pm20) REVERT: E 4995 ASN cc_start: 0.8624 (t0) cc_final: 0.7929 (t0) REVERT: G 31 GLN cc_start: 0.6537 (tt0) cc_final: 0.6304 (tt0) REVERT: H 134 ASP cc_start: 0.7898 (m-30) cc_final: 0.7681 (m-30) REVERT: H 273 HIS cc_start: 0.7094 (m90) cc_final: 0.6523 (m90) REVERT: H 403 MET cc_start: 0.8690 (mtm) cc_final: 0.8177 (ttm) REVERT: H 418 LEU cc_start: 0.8578 (tt) cc_final: 0.8322 (tp) REVERT: H 710 ASP cc_start: 0.8246 (m-30) cc_final: 0.7986 (m-30) REVERT: H 735 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6886 (mm110) REVERT: H 847 SER cc_start: 0.7647 (t) cc_final: 0.7361 (p) REVERT: H 1089 TYR cc_start: 0.8235 (t80) cc_final: 0.7916 (t80) REVERT: H 1141 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7381 (ptp-170) REVERT: H 1293 LEU cc_start: 0.8396 (mt) cc_final: 0.8121 (mt) REVERT: H 1444 GLU cc_start: 0.7683 (mp0) cc_final: 0.7105 (mp0) REVERT: H 1597 MET cc_start: 0.8194 (ttm) cc_final: 0.7975 (ttt) REVERT: H 1601 MET cc_start: 0.8368 (tpp) cc_final: 0.7619 (mtm) REVERT: H 1761 HIS cc_start: 0.8529 (m-70) cc_final: 0.8113 (m-70) REVERT: H 1854 ILE cc_start: 0.9046 (mm) cc_final: 0.8817 (mm) REVERT: H 1930 MET cc_start: 0.7900 (ttt) cc_final: 0.7643 (ttt) REVERT: H 2009 MET cc_start: 0.7510 (ttm) cc_final: 0.6773 (tpp) REVERT: H 2013 PHE cc_start: 0.8551 (t80) cc_final: 0.8351 (t80) REVERT: H 2146 SER cc_start: 0.7604 (p) cc_final: 0.7286 (t) REVERT: H 2171 MET cc_start: 0.8022 (tpp) cc_final: 0.7694 (tpt) REVERT: H 2204 MET cc_start: 0.8398 (mtp) cc_final: 0.8112 (mtp) REVERT: H 2212 MET cc_start: 0.7605 (tpp) cc_final: 0.6962 (tpt) REVERT: H 2239 TYR cc_start: 0.8289 (m-80) cc_final: 0.7970 (m-80) REVERT: H 2251 MET cc_start: 0.9209 (tpt) cc_final: 0.8707 (tpt) REVERT: H 2292 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7772 (mm-40) REVERT: H 2319 TYR cc_start: 0.8074 (m-80) cc_final: 0.7551 (m-10) REVERT: H 2616 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.5873 (mtt180) REVERT: H 2619 MET cc_start: 0.7327 (mmm) cc_final: 0.6577 (mpp) REVERT: H 3664 SER cc_start: 0.9178 (m) cc_final: 0.8877 (t) REVERT: H 3725 MET cc_start: 0.7128 (mtm) cc_final: 0.6439 (mtm) REVERT: H 3772 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8155 (mm-30) REVERT: H 3806 ASP cc_start: 0.7260 (p0) cc_final: 0.5614 (m-30) REVERT: H 4013 ASP cc_start: 0.8408 (m-30) cc_final: 0.8157 (m-30) REVERT: H 4034 MET cc_start: 0.6086 (mtp) cc_final: 0.5114 (mmt) REVERT: H 4136 PHE cc_start: 0.8338 (t80) cc_final: 0.7977 (t80) REVERT: H 4179 MET cc_start: 0.8519 (tmm) cc_final: 0.7414 (tmm) REVERT: H 4187 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7511 (mtt-85) REVERT: H 4191 GLU cc_start: 0.8367 (tt0) cc_final: 0.7916 (tt0) REVERT: H 4555 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7565 (mtt180) REVERT: H 4802 TYR cc_start: 0.6980 (t80) cc_final: 0.6564 (t80) REVERT: H 4837 MET cc_start: 0.9246 (mmm) cc_final: 0.9009 (mmp) REVERT: H 4980 GLU cc_start: 0.7784 (pm20) cc_final: 0.7354 (pm20) REVERT: H 4995 ASN cc_start: 0.8622 (t0) cc_final: 0.7912 (t0) REVERT: J 31 GLN cc_start: 0.6538 (tt0) cc_final: 0.6281 (tt0) REVERT: K 134 ASP cc_start: 0.7894 (m-30) cc_final: 0.7666 (m-30) REVERT: K 255 HIS cc_start: 0.7116 (m90) cc_final: 0.6896 (m-70) REVERT: K 403 MET cc_start: 0.8634 (mtm) cc_final: 0.8242 (mtm) REVERT: K 404 ILE cc_start: 0.9228 (mt) cc_final: 0.8968 (mt) REVERT: K 418 LEU cc_start: 0.8608 (tt) cc_final: 0.8357 (tp) REVERT: K 710 ASP cc_start: 0.8248 (m-30) cc_final: 0.7988 (m-30) REVERT: K 735 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6865 (mm110) REVERT: K 823 LEU cc_start: 0.6695 (mm) cc_final: 0.6491 (mm) REVERT: K 847 SER cc_start: 0.7649 (t) cc_final: 0.7356 (p) REVERT: K 1089 TYR cc_start: 0.8255 (t80) cc_final: 0.7869 (t80) REVERT: K 1141 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7372 (ptp-170) REVERT: K 1152 MET cc_start: 0.7712 (mpp) cc_final: 0.7242 (mpp) REVERT: K 1293 LEU cc_start: 0.8391 (mt) cc_final: 0.8104 (mt) REVERT: K 1444 GLU cc_start: 0.7664 (mp0) cc_final: 0.7108 (mp0) REVERT: K 1601 MET cc_start: 0.8353 (tpp) cc_final: 0.7606 (mtm) REVERT: K 1761 HIS cc_start: 0.8528 (m-70) cc_final: 0.8120 (m-70) REVERT: K 1854 ILE cc_start: 0.9053 (mm) cc_final: 0.8825 (mm) REVERT: K 1930 MET cc_start: 0.7896 (ttt) cc_final: 0.7642 (ttt) REVERT: K 2000 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7549 (mtp85) REVERT: K 2009 MET cc_start: 0.7501 (ttm) cc_final: 0.6768 (tpp) REVERT: K 2013 PHE cc_start: 0.8557 (t80) cc_final: 0.8350 (t80) REVERT: K 2146 SER cc_start: 0.7566 (p) cc_final: 0.7224 (t) REVERT: K 2171 MET cc_start: 0.8072 (tpp) cc_final: 0.7750 (tpt) REVERT: K 2212 MET cc_start: 0.7394 (tpp) cc_final: 0.6811 (tpt) REVERT: K 2239 TYR cc_start: 0.8283 (m-80) cc_final: 0.7919 (m-80) REVERT: K 2292 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7794 (mm-40) REVERT: K 2319 TYR cc_start: 0.8079 (m-80) cc_final: 0.7569 (m-10) REVERT: K 2616 ARG cc_start: 0.7028 (mtp-110) cc_final: 0.5893 (mtt180) REVERT: K 3664 SER cc_start: 0.9168 (m) cc_final: 0.8874 (t) REVERT: K 3725 MET cc_start: 0.7114 (mtm) cc_final: 0.6465 (mtm) REVERT: K 3753 MET cc_start: 0.6778 (tpp) cc_final: 0.6274 (tpt) REVERT: K 3772 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8140 (mm-30) REVERT: K 3804 ASN cc_start: 0.7041 (m-40) cc_final: 0.6525 (m110) REVERT: K 3806 ASP cc_start: 0.7217 (p0) cc_final: 0.5568 (m-30) REVERT: K 4013 ASP cc_start: 0.8410 (m-30) cc_final: 0.8167 (m-30) REVERT: K 4032 ASN cc_start: 0.7061 (m-40) cc_final: 0.6531 (t0) REVERT: K 4034 MET cc_start: 0.5875 (mtt) cc_final: 0.5276 (mmt) REVERT: K 4136 PHE cc_start: 0.8349 (t80) cc_final: 0.7882 (t80) REVERT: K 4179 MET cc_start: 0.8431 (tmm) cc_final: 0.7506 (tmm) REVERT: K 4187 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7469 (mtt-85) REVERT: K 4191 GLU cc_start: 0.8378 (tt0) cc_final: 0.7870 (tt0) REVERT: K 4555 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7576 (mtt180) REVERT: K 4802 TYR cc_start: 0.6981 (t80) cc_final: 0.6567 (t80) REVERT: K 4837 MET cc_start: 0.9248 (mmm) cc_final: 0.9010 (mmp) REVERT: K 4980 GLU cc_start: 0.7721 (pm20) cc_final: 0.7310 (pm20) REVERT: K 4995 ASN cc_start: 0.8617 (t0) cc_final: 0.7924 (t0) REVERT: L 1 MET cc_start: 0.7187 (mtp) cc_final: 0.6781 (mtt) outliers start: 1 outliers final: 1 residues processed: 2246 average time/residue: 0.8418 time to fit residues: 3407.5461 Evaluate side-chains 1978 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1977 time to evaluate : 8.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 961 optimal weight: 0.8980 chunk 620 optimal weight: 0.8980 chunk 927 optimal weight: 0.9990 chunk 468 optimal weight: 0.5980 chunk 305 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 chunk 987 optimal weight: 0.9990 chunk 1058 optimal weight: 50.0000 chunk 768 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 1221 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1776 HIS B1862 GLN B2096 GLN B2194 GLN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3766 HIS B3767 ASN B3776 GLN ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4218 ASN B4648 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1776 HIS E1862 GLN E2096 GLN ** E2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2194 GLN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3766 HIS E3767 ASN ** E3804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4029 ASN E4218 ASN E4648 HIS ** E4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2194 GLN H2261 ASN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3766 HIS H3767 ASN ** H3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H4218 ASN H4648 HIS ** H4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1776 HIS K1862 GLN K2194 GLN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3766 HIS K3767 ASN ** K3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4218 ASN K4648 HIS ** K4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 113972 Z= 0.172 Angle : 0.566 13.319 155608 Z= 0.278 Chirality : 0.038 0.204 18776 Planarity : 0.004 0.083 20052 Dihedral : 3.926 21.150 16964 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.02 % Allowed : 0.54 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.07), residues: 14452 helix: 2.08 (0.06), residues: 7212 sheet: -0.75 (0.14), residues: 1300 loop : -1.30 (0.08), residues: 5940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H1143 HIS 0.017 0.001 HIS H4981 PHE 0.028 0.002 PHE B1549 TYR 0.030 0.001 TYR K4713 ARG 0.008 0.001 ARG K5027 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2292 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2290 time to evaluate : 8.003 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: B 418 LEU cc_start: 0.8498 (tt) cc_final: 0.8235 (tp) REVERT: B 634 GLN cc_start: 0.8926 (mm110) cc_final: 0.8151 (mt0) REVERT: B 710 ASP cc_start: 0.8133 (m-30) cc_final: 0.7925 (m-30) REVERT: B 735 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6982 (mm110) REVERT: B 799 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6887 (mp0) REVERT: B 847 SER cc_start: 0.7700 (t) cc_final: 0.7414 (p) REVERT: B 1100 MET cc_start: 0.7502 (ptt) cc_final: 0.7280 (ptt) REVERT: B 1141 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7414 (ptp-170) REVERT: B 1245 PHE cc_start: 0.8770 (m-80) cc_final: 0.8112 (m-80) REVERT: B 1444 GLU cc_start: 0.7635 (mp0) cc_final: 0.7013 (mp0) REVERT: B 1446 SER cc_start: 0.8587 (p) cc_final: 0.8300 (m) REVERT: B 1601 MET cc_start: 0.8160 (tpp) cc_final: 0.7085 (mtm) REVERT: B 1648 MET cc_start: 0.7703 (ttm) cc_final: 0.7467 (ttp) REVERT: B 1721 GLU cc_start: 0.8368 (tt0) cc_final: 0.7645 (tp30) REVERT: B 1854 ILE cc_start: 0.9002 (mm) cc_final: 0.8785 (mm) REVERT: B 1999 PHE cc_start: 0.8626 (t80) cc_final: 0.8380 (t80) REVERT: B 2009 MET cc_start: 0.7593 (ttm) cc_final: 0.6673 (tpp) REVERT: B 2013 PHE cc_start: 0.8204 (t80) cc_final: 0.7932 (t80) REVERT: B 2146 SER cc_start: 0.7450 (p) cc_final: 0.7068 (t) REVERT: B 2171 MET cc_start: 0.7968 (tpp) cc_final: 0.7483 (tpt) REVERT: B 2239 TYR cc_start: 0.8183 (m-80) cc_final: 0.7853 (m-80) REVERT: B 2251 MET cc_start: 0.9276 (tpt) cc_final: 0.8912 (tpt) REVERT: B 2292 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7677 (mm-40) REVERT: B 2319 TYR cc_start: 0.7894 (m-80) cc_final: 0.7425 (m-10) REVERT: B 2616 ARG cc_start: 0.7014 (mtp-110) cc_final: 0.5889 (mtt180) REVERT: B 3664 SER cc_start: 0.8974 (m) cc_final: 0.8672 (t) REVERT: B 3725 MET cc_start: 0.7112 (mtm) cc_final: 0.6597 (mtm) REVERT: B 3806 ASP cc_start: 0.6992 (p0) cc_final: 0.5421 (m-30) REVERT: B 4013 ASP cc_start: 0.8332 (m-30) cc_final: 0.8058 (m-30) REVERT: B 4029 ASN cc_start: 0.7380 (t0) cc_final: 0.7139 (t0) REVERT: B 4034 MET cc_start: 0.5996 (mtt) cc_final: 0.5392 (mmt) REVERT: B 4170 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8522 (tpp80) REVERT: B 4179 MET cc_start: 0.8551 (tmm) cc_final: 0.7522 (tmm) REVERT: B 4187 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7374 (mtt-85) REVERT: B 4555 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.7680 (mtt180) REVERT: B 4796 MET cc_start: 0.8022 (mmt) cc_final: 0.7701 (tpp) REVERT: B 4802 TYR cc_start: 0.6779 (t80) cc_final: 0.6445 (t80) REVERT: B 4837 MET cc_start: 0.9176 (mmm) cc_final: 0.8924 (mmp) REVERT: B 4980 GLU cc_start: 0.6482 (mp0) cc_final: 0.5905 (mp0) REVERT: B 4995 ASN cc_start: 0.8589 (t0) cc_final: 0.7914 (t0) REVERT: E 167 ASP cc_start: 0.8930 (m-30) cc_final: 0.8320 (p0) REVERT: E 418 LEU cc_start: 0.8521 (tt) cc_final: 0.8254 (tp) REVERT: E 634 GLN cc_start: 0.8910 (mm110) cc_final: 0.8383 (mt0) REVERT: E 710 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30) REVERT: E 735 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6869 (mm110) REVERT: E 847 SER cc_start: 0.7698 (t) cc_final: 0.7416 (p) REVERT: E 1141 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7350 (ptp-170) REVERT: E 1245 PHE cc_start: 0.8728 (m-80) cc_final: 0.8162 (m-80) REVERT: E 1444 GLU cc_start: 0.7615 (mp0) cc_final: 0.6990 (mp0) REVERT: E 1446 SER cc_start: 0.8599 (p) cc_final: 0.8219 (m) REVERT: E 1563 GLN cc_start: 0.7610 (mt0) cc_final: 0.7305 (mm-40) REVERT: E 1599 MET cc_start: 0.5600 (ttt) cc_final: 0.5347 (ttt) REVERT: E 1601 MET cc_start: 0.8417 (tpp) cc_final: 0.7522 (mtm) REVERT: E 1648 MET cc_start: 0.7734 (ttm) cc_final: 0.7505 (ttp) REVERT: E 1703 LEU cc_start: 0.8914 (tp) cc_final: 0.8476 (mp) REVERT: E 1854 ILE cc_start: 0.9014 (mm) cc_final: 0.8720 (mm) REVERT: E 1999 PHE cc_start: 0.8625 (t80) cc_final: 0.8374 (t80) REVERT: E 2000 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7332 (mtp85) REVERT: E 2009 MET cc_start: 0.7589 (ttm) cc_final: 0.6674 (tpp) REVERT: E 2013 PHE cc_start: 0.8452 (t80) cc_final: 0.8150 (t80) REVERT: E 2146 SER cc_start: 0.7459 (p) cc_final: 0.7087 (t) REVERT: E 2171 MET cc_start: 0.7897 (tpp) cc_final: 0.7499 (tpt) REVERT: E 2209 MET cc_start: 0.7634 (ttm) cc_final: 0.7371 (ttm) REVERT: E 2239 TYR cc_start: 0.8194 (m-80) cc_final: 0.7852 (m-80) REVERT: E 2251 MET cc_start: 0.9276 (tpt) cc_final: 0.8873 (tpt) REVERT: E 2292 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7676 (mm-40) REVERT: E 2319 TYR cc_start: 0.7944 (m-80) cc_final: 0.7481 (m-10) REVERT: E 2616 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.5882 (mtt180) REVERT: E 3664 SER cc_start: 0.9007 (m) cc_final: 0.8685 (t) REVERT: E 3725 MET cc_start: 0.7036 (mtm) cc_final: 0.6349 (mtm) REVERT: E 3772 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8134 (mm-30) REVERT: E 3804 ASN cc_start: 0.6922 (m-40) cc_final: 0.6670 (m-40) REVERT: E 3806 ASP cc_start: 0.7000 (p0) cc_final: 0.5471 (m-30) REVERT: E 4013 ASP cc_start: 0.8331 (m-30) cc_final: 0.8082 (m-30) REVERT: E 4034 MET cc_start: 0.6213 (mtp) cc_final: 0.5306 (mmt) REVERT: E 4136 PHE cc_start: 0.8308 (t80) cc_final: 0.8019 (t80) REVERT: E 4179 MET cc_start: 0.8500 (tmm) cc_final: 0.7327 (tmm) REVERT: E 4187 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7389 (mtt-85) REVERT: E 4191 GLU cc_start: 0.8467 (tt0) cc_final: 0.8014 (tt0) REVERT: E 4555 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7680 (mtt180) REVERT: E 4796 MET cc_start: 0.8022 (mmt) cc_final: 0.7700 (tpp) REVERT: E 4802 TYR cc_start: 0.6731 (t80) cc_final: 0.6395 (t80) REVERT: E 4837 MET cc_start: 0.9169 (mmm) cc_final: 0.8920 (mmp) REVERT: E 4980 GLU cc_start: 0.7649 (pm20) cc_final: 0.7376 (pm20) REVERT: E 4995 ASN cc_start: 0.8576 (t0) cc_final: 0.7919 (t0) REVERT: H 418 LEU cc_start: 0.8500 (tt) cc_final: 0.8228 (tp) REVERT: H 634 GLN cc_start: 0.8888 (mm110) cc_final: 0.8372 (mt0) REVERT: H 710 ASP cc_start: 0.8105 (m-30) cc_final: 0.7901 (m-30) REVERT: H 735 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6934 (mm110) REVERT: H 847 SER cc_start: 0.7707 (t) cc_final: 0.7427 (p) REVERT: H 1100 MET cc_start: 0.7473 (ptt) cc_final: 0.7183 (ptt) REVERT: H 1141 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7365 (ptp-170) REVERT: H 1245 PHE cc_start: 0.8728 (m-80) cc_final: 0.8136 (m-80) REVERT: H 1444 GLU cc_start: 0.7616 (mp0) cc_final: 0.7002 (mp0) REVERT: H 1446 SER cc_start: 0.8595 (p) cc_final: 0.8321 (m) REVERT: H 1563 GLN cc_start: 0.7617 (mt0) cc_final: 0.7304 (mm-40) REVERT: H 1599 MET cc_start: 0.5574 (ttt) cc_final: 0.5334 (ttt) REVERT: H 1601 MET cc_start: 0.8416 (tpp) cc_final: 0.7522 (mtm) REVERT: H 1648 MET cc_start: 0.7751 (ttm) cc_final: 0.7511 (ttp) REVERT: H 1854 ILE cc_start: 0.9009 (mm) cc_final: 0.8722 (mm) REVERT: H 1999 PHE cc_start: 0.8626 (t80) cc_final: 0.8378 (t80) REVERT: H 2000 ARG cc_start: 0.7545 (mtp85) cc_final: 0.7323 (mtp85) REVERT: H 2009 MET cc_start: 0.7544 (ttm) cc_final: 0.6642 (tpp) REVERT: H 2013 PHE cc_start: 0.8451 (t80) cc_final: 0.8180 (t80) REVERT: H 2146 SER cc_start: 0.7465 (p) cc_final: 0.7084 (t) REVERT: H 2171 MET cc_start: 0.7903 (tpp) cc_final: 0.7483 (tpt) REVERT: H 2239 TYR cc_start: 0.8198 (m-80) cc_final: 0.7911 (m-80) REVERT: H 2251 MET cc_start: 0.9185 (tpt) cc_final: 0.8833 (tpt) REVERT: H 2292 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7670 (mm-40) REVERT: H 2319 TYR cc_start: 0.7887 (m-80) cc_final: 0.7408 (m-10) REVERT: H 2616 ARG cc_start: 0.7026 (mtp-110) cc_final: 0.5869 (mtt180) REVERT: H 3664 SER cc_start: 0.9005 (m) cc_final: 0.8696 (t) REVERT: H 3725 MET cc_start: 0.7034 (mtm) cc_final: 0.6363 (mtm) REVERT: H 3772 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8112 (mm-30) REVERT: H 3846 ASN cc_start: 0.8235 (p0) cc_final: 0.7801 (m-40) REVERT: H 4013 ASP cc_start: 0.8327 (m-30) cc_final: 0.8075 (m-30) REVERT: H 4034 MET cc_start: 0.6076 (mtp) cc_final: 0.5183 (mmt) REVERT: H 4136 PHE cc_start: 0.8297 (t80) cc_final: 0.7998 (t80) REVERT: H 4179 MET cc_start: 0.8537 (tmm) cc_final: 0.7493 (tmm) REVERT: H 4187 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: H 4191 GLU cc_start: 0.8463 (tt0) cc_final: 0.8002 (tt0) REVERT: H 4555 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.7673 (mtt180) REVERT: H 4796 MET cc_start: 0.8029 (mmt) cc_final: 0.7701 (tpp) REVERT: H 4802 TYR cc_start: 0.6771 (t80) cc_final: 0.6434 (t80) REVERT: H 4837 MET cc_start: 0.9173 (mmm) cc_final: 0.8926 (mmp) REVERT: H 4980 GLU cc_start: 0.7548 (pm20) cc_final: 0.7147 (pm20) REVERT: H 4995 ASN cc_start: 0.8575 (t0) cc_final: 0.7911 (t0) REVERT: K 418 LEU cc_start: 0.8533 (tt) cc_final: 0.8268 (tp) REVERT: K 634 GLN cc_start: 0.8910 (mm110) cc_final: 0.8378 (mt0) REVERT: K 710 ASP cc_start: 0.8115 (m-30) cc_final: 0.7912 (m-30) REVERT: K 735 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6872 (mm110) REVERT: K 847 SER cc_start: 0.7703 (t) cc_final: 0.7432 (p) REVERT: K 1141 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7377 (ptp-170) REVERT: K 1245 PHE cc_start: 0.8727 (m-80) cc_final: 0.8136 (m-80) REVERT: K 1444 GLU cc_start: 0.7604 (mp0) cc_final: 0.7004 (mp0) REVERT: K 1446 SER cc_start: 0.8603 (p) cc_final: 0.8316 (m) REVERT: K 1599 MET cc_start: 0.5561 (ttt) cc_final: 0.5323 (ttt) REVERT: K 1601 MET cc_start: 0.8412 (tpp) cc_final: 0.7534 (mtm) REVERT: K 1854 ILE cc_start: 0.9017 (mm) cc_final: 0.8723 (mm) REVERT: K 1999 PHE cc_start: 0.8707 (t80) cc_final: 0.8421 (t80) REVERT: K 2000 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7570 (mtp85) REVERT: K 2009 MET cc_start: 0.7421 (ttm) cc_final: 0.6578 (tpp) REVERT: K 2013 PHE cc_start: 0.8438 (t80) cc_final: 0.8138 (t80) REVERT: K 2146 SER cc_start: 0.7444 (p) cc_final: 0.7085 (t) REVERT: K 2171 MET cc_start: 0.7975 (tpp) cc_final: 0.7571 (tpt) REVERT: K 2239 TYR cc_start: 0.8172 (m-80) cc_final: 0.7879 (m-80) REVERT: K 2251 MET cc_start: 0.9076 (tpt) cc_final: 0.8593 (tpt) REVERT: K 2292 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7674 (mm-40) REVERT: K 2319 TYR cc_start: 0.7893 (m-80) cc_final: 0.7423 (m-10) REVERT: K 2616 ARG cc_start: 0.6997 (mtp-110) cc_final: 0.5883 (mtt180) REVERT: K 3633 ARG cc_start: 0.7248 (tmt-80) cc_final: 0.7041 (tpt90) REVERT: K 3664 SER cc_start: 0.9000 (m) cc_final: 0.8689 (t) REVERT: K 3725 MET cc_start: 0.7063 (mtm) cc_final: 0.6383 (mtm) REVERT: K 3753 MET cc_start: 0.6749 (tpp) cc_final: 0.6275 (tpp) REVERT: K 3772 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8087 (mm-30) REVERT: K 3846 ASN cc_start: 0.8239 (p0) cc_final: 0.7797 (m-40) REVERT: K 4013 ASP cc_start: 0.8335 (m-30) cc_final: 0.8083 (m-30) REVERT: K 4029 ASN cc_start: 0.7368 (t0) cc_final: 0.7132 (t0) REVERT: K 4032 ASN cc_start: 0.6734 (m-40) cc_final: 0.6281 (t0) REVERT: K 4034 MET cc_start: 0.5626 (mtt) cc_final: 0.4885 (mmt) REVERT: K 4136 PHE cc_start: 0.8309 (t80) cc_final: 0.7962 (t80) REVERT: K 4179 MET cc_start: 0.8518 (tmm) cc_final: 0.7477 (tmm) REVERT: K 4187 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7688 (mtt-85) REVERT: K 4191 GLU cc_start: 0.8466 (tt0) cc_final: 0.7957 (tt0) REVERT: K 4555 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.7684 (mtt180) REVERT: K 4796 MET cc_start: 0.8036 (mmt) cc_final: 0.7709 (tpp) REVERT: K 4802 TYR cc_start: 0.6770 (t80) cc_final: 0.6437 (t80) REVERT: K 4837 MET cc_start: 0.9182 (mmm) cc_final: 0.8930 (mmp) REVERT: K 4980 GLU cc_start: 0.7613 (pm20) cc_final: 0.7366 (pm20) REVERT: K 4995 ASN cc_start: 0.8571 (t0) cc_final: 0.7922 (t0) REVERT: L 1 MET cc_start: 0.7201 (mtp) cc_final: 0.6854 (mtt) outliers start: 2 outliers final: 0 residues processed: 2290 average time/residue: 0.8370 time to fit residues: 3457.4518 Evaluate side-chains 1995 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1995 time to evaluate : 8.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1413 optimal weight: 0.4980 chunk 1488 optimal weight: 10.0000 chunk 1358 optimal weight: 1.9990 chunk 1447 optimal weight: 20.0000 chunk 871 optimal weight: 1.9990 chunk 630 optimal weight: 8.9990 chunk 1136 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 1308 optimal weight: 30.0000 chunk 1369 optimal weight: 0.0470 chunk 1442 optimal weight: 20.0000 overall best weight: 2.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 681 HIS ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1761 HIS B1776 HIS B1862 GLN B2096 GLN ** B2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2261 ASN B2521 HIS ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 ASN B3776 GLN ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 681 HIS E1761 HIS E1776 HIS E1862 GLN E1950 GLN E2096 GLN ** E2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2261 ASN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3767 ASN ** E3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 624 ASN H 681 HIS ** H1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1761 HIS H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2247 ASN H2261 ASN H2521 HIS ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3767 ASN ** H4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 624 ASN K 681 HIS K1761 HIS K1776 HIS K1862 GLN K1950 GLN ** K2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2247 ASN K2261 ASN K2521 HIS ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3767 ASN ** K3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 113972 Z= 0.354 Angle : 0.688 12.719 155608 Z= 0.347 Chirality : 0.042 0.274 18776 Planarity : 0.005 0.120 20052 Dihedral : 4.313 21.245 16964 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.07), residues: 14452 helix: 1.75 (0.06), residues: 7188 sheet: -0.81 (0.14), residues: 1340 loop : -1.44 (0.08), residues: 5924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H1143 HIS 0.015 0.001 HIS K4981 PHE 0.029 0.002 PHE H5020 TYR 0.035 0.002 TYR B4986 ARG 0.008 0.001 ARG B5027 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2250 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2250 time to evaluate : 8.810 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: B 134 ASP cc_start: 0.7896 (m-30) cc_final: 0.7692 (m-30) REVERT: B 167 ASP cc_start: 0.9029 (m-30) cc_final: 0.8193 (p0) REVERT: B 404 ILE cc_start: 0.9255 (mt) cc_final: 0.9047 (mt) REVERT: B 418 LEU cc_start: 0.8558 (tt) cc_final: 0.8317 (tp) REVERT: B 710 ASP cc_start: 0.8173 (m-30) cc_final: 0.7862 (m-30) REVERT: B 735 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6957 (mm110) REVERT: B 847 SER cc_start: 0.7658 (t) cc_final: 0.7395 (p) REVERT: B 1089 TYR cc_start: 0.8204 (t80) cc_final: 0.7814 (t80) REVERT: B 1141 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7362 (ptp-170) REVERT: B 1152 MET cc_start: 0.7792 (mpp) cc_final: 0.7143 (mpp) REVERT: B 1293 LEU cc_start: 0.8510 (mp) cc_final: 0.8170 (mp) REVERT: B 1444 GLU cc_start: 0.7703 (mp0) cc_final: 0.7113 (mp0) REVERT: B 1446 SER cc_start: 0.8543 (p) cc_final: 0.8192 (m) REVERT: B 1597 MET cc_start: 0.8271 (ttm) cc_final: 0.8005 (ttt) REVERT: B 1601 MET cc_start: 0.8297 (tpp) cc_final: 0.7162 (mtm) REVERT: B 1761 HIS cc_start: 0.8508 (m-70) cc_final: 0.8210 (m90) REVERT: B 1854 ILE cc_start: 0.9085 (mm) cc_final: 0.8859 (mm) REVERT: B 1930 MET cc_start: 0.7820 (ttt) cc_final: 0.7580 (ttt) REVERT: B 1999 PHE cc_start: 0.8758 (t80) cc_final: 0.8421 (t80) REVERT: B 2000 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7785 (mtp85) REVERT: B 2009 MET cc_start: 0.7426 (ttm) cc_final: 0.6625 (tpp) REVERT: B 2146 SER cc_start: 0.7569 (p) cc_final: 0.7222 (t) REVERT: B 2171 MET cc_start: 0.7921 (tpp) cc_final: 0.6550 (tpt) REVERT: B 2212 MET cc_start: 0.7398 (tpp) cc_final: 0.6805 (tpt) REVERT: B 2239 TYR cc_start: 0.8252 (m-80) cc_final: 0.7928 (m-80) REVERT: B 2251 MET cc_start: 0.9153 (tpt) cc_final: 0.8735 (tpt) REVERT: B 2319 TYR cc_start: 0.8023 (m-80) cc_final: 0.7501 (m-10) REVERT: B 2616 ARG cc_start: 0.7084 (mtp-110) cc_final: 0.6023 (ptt180) REVERT: B 3634 MET cc_start: 0.8185 (mmp) cc_final: 0.7813 (mmm) REVERT: B 3664 SER cc_start: 0.9169 (m) cc_final: 0.8752 (t) REVERT: B 3669 MET cc_start: 0.7660 (ttt) cc_final: 0.6554 (ttp) REVERT: B 3725 MET cc_start: 0.7241 (mtm) cc_final: 0.6597 (mtm) REVERT: B 3806 ASP cc_start: 0.7047 (p0) cc_final: 0.5839 (m-30) REVERT: B 4013 ASP cc_start: 0.8412 (m-30) cc_final: 0.8135 (m-30) REVERT: B 4034 MET cc_start: 0.6049 (mtt) cc_final: 0.5431 (mmm) REVERT: B 4170 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8509 (tpp80) REVERT: B 4179 MET cc_start: 0.8539 (tmm) cc_final: 0.7409 (tmm) REVERT: B 4187 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7505 (mtt-85) REVERT: B 4555 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.7625 (mtt180) REVERT: B 4796 MET cc_start: 0.8193 (mmt) cc_final: 0.7838 (tpp) REVERT: B 4802 TYR cc_start: 0.6937 (t80) cc_final: 0.6564 (t80) REVERT: B 4837 MET cc_start: 0.9253 (mmm) cc_final: 0.8769 (mmt) REVERT: B 4980 GLU cc_start: 0.6750 (mp0) cc_final: 0.6174 (mp0) REVERT: B 4995 ASN cc_start: 0.8722 (t0) cc_final: 0.8070 (t0) REVERT: E 113 HIS cc_start: 0.8510 (t70) cc_final: 0.8175 (t70) REVERT: E 134 ASP cc_start: 0.7866 (m-30) cc_final: 0.7666 (m-30) REVERT: E 167 ASP cc_start: 0.9123 (m-30) cc_final: 0.8875 (m-30) REVERT: E 273 HIS cc_start: 0.7116 (m90) cc_final: 0.6506 (m90) REVERT: E 418 LEU cc_start: 0.8571 (tt) cc_final: 0.8325 (tp) REVERT: E 710 ASP cc_start: 0.8154 (m-30) cc_final: 0.7856 (m-30) REVERT: E 735 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7025 (mm110) REVERT: E 847 SER cc_start: 0.7653 (t) cc_final: 0.7391 (p) REVERT: E 1089 TYR cc_start: 0.8177 (t80) cc_final: 0.7796 (t80) REVERT: E 1141 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7392 (ptp-170) REVERT: E 1152 MET cc_start: 0.7639 (mpp) cc_final: 0.7021 (mpp) REVERT: E 1293 LEU cc_start: 0.8542 (mp) cc_final: 0.8199 (mp) REVERT: E 1444 GLU cc_start: 0.7690 (mp0) cc_final: 0.7088 (mp0) REVERT: E 1446 SER cc_start: 0.8546 (p) cc_final: 0.8128 (m) REVERT: E 1597 MET cc_start: 0.8231 (ttm) cc_final: 0.7971 (ttt) REVERT: E 1601 MET cc_start: 0.8368 (tpp) cc_final: 0.7451 (mtm) REVERT: E 1671 ARG cc_start: 0.7361 (mtm110) cc_final: 0.5617 (ttt-90) REVERT: E 1761 HIS cc_start: 0.8504 (m-70) cc_final: 0.8205 (m90) REVERT: E 1854 ILE cc_start: 0.9058 (mm) cc_final: 0.8794 (mm) REVERT: E 1999 PHE cc_start: 0.8776 (t80) cc_final: 0.8401 (t80) REVERT: E 2000 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7393 (mtp85) REVERT: E 2009 MET cc_start: 0.7478 (ttm) cc_final: 0.6615 (tpp) REVERT: E 2146 SER cc_start: 0.7553 (p) cc_final: 0.7191 (t) REVERT: E 2171 MET cc_start: 0.8003 (tpp) cc_final: 0.6559 (tpt) REVERT: E 2209 MET cc_start: 0.7838 (ttm) cc_final: 0.7603 (ttm) REVERT: E 2212 MET cc_start: 0.7415 (tpp) cc_final: 0.6833 (tpt) REVERT: E 2239 TYR cc_start: 0.8243 (m-80) cc_final: 0.7931 (m-80) REVERT: E 2251 MET cc_start: 0.9277 (tpt) cc_final: 0.8788 (tpt) REVERT: E 2319 TYR cc_start: 0.8021 (m-80) cc_final: 0.7497 (m-10) REVERT: E 2616 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6021 (ptt180) REVERT: E 3634 MET cc_start: 0.8175 (mmp) cc_final: 0.7832 (mmm) REVERT: E 3663 HIS cc_start: 0.7575 (p90) cc_final: 0.7360 (p90) REVERT: E 3664 SER cc_start: 0.9165 (m) cc_final: 0.8834 (t) REVERT: E 3725 MET cc_start: 0.7141 (mtm) cc_final: 0.6458 (mtm) REVERT: E 3772 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8205 (mm-30) REVERT: E 3994 MET cc_start: 0.4889 (tpt) cc_final: 0.4376 (tpp) REVERT: E 4013 ASP cc_start: 0.8411 (m-30) cc_final: 0.8134 (m-30) REVERT: E 4034 MET cc_start: 0.6403 (mtp) cc_final: 0.5395 (mmt) REVERT: E 4136 PHE cc_start: 0.8326 (t80) cc_final: 0.7983 (t80) REVERT: E 4179 MET cc_start: 0.8501 (tmm) cc_final: 0.7377 (tmm) REVERT: E 4187 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7519 (mtt-85) REVERT: E 4191 GLU cc_start: 0.8445 (tt0) cc_final: 0.7918 (tt0) REVERT: E 4555 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.7623 (mtt180) REVERT: E 4796 MET cc_start: 0.8153 (mmt) cc_final: 0.7800 (tpp) REVERT: E 4802 TYR cc_start: 0.6912 (t80) cc_final: 0.6514 (t80) REVERT: E 4837 MET cc_start: 0.9249 (mmm) cc_final: 0.8765 (mmt) REVERT: E 4980 GLU cc_start: 0.7835 (pm20) cc_final: 0.7419 (pm20) REVERT: E 4995 ASN cc_start: 0.8635 (t0) cc_final: 0.8031 (t0) REVERT: H 113 HIS cc_start: 0.8506 (t70) cc_final: 0.8168 (t70) REVERT: H 273 HIS cc_start: 0.7108 (m90) cc_final: 0.6510 (m90) REVERT: H 418 LEU cc_start: 0.8583 (tt) cc_final: 0.8327 (tp) REVERT: H 710 ASP cc_start: 0.8151 (m-30) cc_final: 0.7853 (m-30) REVERT: H 735 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7003 (mm110) REVERT: H 847 SER cc_start: 0.7667 (t) cc_final: 0.7405 (p) REVERT: H 1141 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7397 (ptp-170) REVERT: H 1293 LEU cc_start: 0.8535 (mp) cc_final: 0.8189 (mp) REVERT: H 1444 GLU cc_start: 0.7693 (mp0) cc_final: 0.7102 (mp0) REVERT: H 1446 SER cc_start: 0.8583 (p) cc_final: 0.8242 (m) REVERT: H 1601 MET cc_start: 0.8365 (tpp) cc_final: 0.7442 (mtm) REVERT: H 1671 ARG cc_start: 0.7353 (mtm110) cc_final: 0.5614 (ttt-90) REVERT: H 1761 HIS cc_start: 0.8519 (m-70) cc_final: 0.8213 (m90) REVERT: H 1854 ILE cc_start: 0.9046 (mm) cc_final: 0.8793 (mm) REVERT: H 1930 MET cc_start: 0.7815 (ttt) cc_final: 0.7545 (ttt) REVERT: H 1999 PHE cc_start: 0.8778 (t80) cc_final: 0.8403 (t80) REVERT: H 2000 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7394 (mtp85) REVERT: H 2009 MET cc_start: 0.7475 (ttm) cc_final: 0.6640 (tpp) REVERT: H 2146 SER cc_start: 0.7581 (p) cc_final: 0.7220 (t) REVERT: H 2171 MET cc_start: 0.7982 (tpp) cc_final: 0.6560 (tpt) REVERT: H 2212 MET cc_start: 0.7497 (tpp) cc_final: 0.6957 (tpt) REVERT: H 2239 TYR cc_start: 0.8255 (m-80) cc_final: 0.7928 (m-80) REVERT: H 2292 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7714 (mm-40) REVERT: H 2319 TYR cc_start: 0.8016 (m-80) cc_final: 0.7489 (m-10) REVERT: H 2616 ARG cc_start: 0.7083 (mtp-110) cc_final: 0.6029 (ptt180) REVERT: H 3634 MET cc_start: 0.8170 (mmp) cc_final: 0.7829 (mmm) REVERT: H 3664 SER cc_start: 0.9185 (m) cc_final: 0.8892 (t) REVERT: H 3725 MET cc_start: 0.7144 (mtm) cc_final: 0.6463 (mtm) REVERT: H 3772 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8199 (mm-30) REVERT: H 3994 MET cc_start: 0.4888 (tpt) cc_final: 0.4373 (tpp) REVERT: H 4013 ASP cc_start: 0.8358 (m-30) cc_final: 0.8090 (m-30) REVERT: H 4034 MET cc_start: 0.6256 (mtp) cc_final: 0.5282 (mmt) REVERT: H 4136 PHE cc_start: 0.8307 (t80) cc_final: 0.7971 (t80) REVERT: H 4179 MET cc_start: 0.8566 (tmm) cc_final: 0.7446 (tmm) REVERT: H 4187 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7509 (mtt-85) REVERT: H 4191 GLU cc_start: 0.8439 (tt0) cc_final: 0.7917 (tt0) REVERT: H 4555 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.7613 (mtt180) REVERT: H 4796 MET cc_start: 0.8151 (mmt) cc_final: 0.7801 (tpp) REVERT: H 4802 TYR cc_start: 0.6928 (t80) cc_final: 0.6556 (t80) REVERT: H 4837 MET cc_start: 0.9254 (mmm) cc_final: 0.8776 (mmt) REVERT: H 4877 MET cc_start: 0.7451 (ttp) cc_final: 0.6629 (tmm) REVERT: H 4980 GLU cc_start: 0.7785 (pm20) cc_final: 0.7182 (pm20) REVERT: H 4995 ASN cc_start: 0.8626 (t0) cc_final: 0.7960 (t0) REVERT: K 113 HIS cc_start: 0.8446 (t70) cc_final: 0.8148 (t70) REVERT: K 134 ASP cc_start: 0.7917 (m-30) cc_final: 0.7693 (m-30) REVERT: K 273 HIS cc_start: 0.7115 (m90) cc_final: 0.6547 (m90) REVERT: K 418 LEU cc_start: 0.8578 (tt) cc_final: 0.8346 (tp) REVERT: K 710 ASP cc_start: 0.8166 (m-30) cc_final: 0.7863 (m-30) REVERT: K 735 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6926 (mm110) REVERT: K 847 SER cc_start: 0.7669 (t) cc_final: 0.7409 (p) REVERT: K 1089 TYR cc_start: 0.8182 (t80) cc_final: 0.7810 (t80) REVERT: K 1141 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7382 (ptp-170) REVERT: K 1152 MET cc_start: 0.7626 (mpp) cc_final: 0.6991 (mpp) REVERT: K 1293 LEU cc_start: 0.8540 (mp) cc_final: 0.8276 (mp) REVERT: K 1444 GLU cc_start: 0.7694 (mp0) cc_final: 0.7102 (mp0) REVERT: K 1446 SER cc_start: 0.8590 (p) cc_final: 0.8246 (m) REVERT: K 1601 MET cc_start: 0.8361 (tpp) cc_final: 0.7456 (mtm) REVERT: K 1761 HIS cc_start: 0.8521 (m-70) cc_final: 0.8224 (m90) REVERT: K 1854 ILE cc_start: 0.9060 (mm) cc_final: 0.8798 (mm) REVERT: K 1999 PHE cc_start: 0.8704 (t80) cc_final: 0.8401 (t80) REVERT: K 2000 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7530 (mtp85) REVERT: K 2009 MET cc_start: 0.7462 (ttm) cc_final: 0.6629 (tpp) REVERT: K 2146 SER cc_start: 0.7558 (p) cc_final: 0.7228 (t) REVERT: K 2171 MET cc_start: 0.8048 (tpp) cc_final: 0.6684 (tpt) REVERT: K 2212 MET cc_start: 0.7380 (tpp) cc_final: 0.6918 (tpt) REVERT: K 2239 TYR cc_start: 0.8248 (m-80) cc_final: 0.7898 (m-80) REVERT: K 2319 TYR cc_start: 0.8024 (m-80) cc_final: 0.7510 (m-10) REVERT: K 2616 ARG cc_start: 0.7065 (mtp-110) cc_final: 0.6003 (ptt180) REVERT: K 3634 MET cc_start: 0.8123 (mmp) cc_final: 0.7755 (mmm) REVERT: K 3664 SER cc_start: 0.9170 (m) cc_final: 0.8880 (t) REVERT: K 3725 MET cc_start: 0.7168 (mtm) cc_final: 0.6484 (mtm) REVERT: K 3753 MET cc_start: 0.6755 (tpp) cc_final: 0.6238 (tpt) REVERT: K 3772 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8076 (mm-30) REVERT: K 3994 MET cc_start: 0.4890 (tpt) cc_final: 0.4369 (tpp) REVERT: K 4013 ASP cc_start: 0.8362 (m-30) cc_final: 0.8096 (m-30) REVERT: K 4032 ASN cc_start: 0.7011 (m-40) cc_final: 0.6519 (t0) REVERT: K 4034 MET cc_start: 0.5888 (mtt) cc_final: 0.5318 (mmt) REVERT: K 4136 PHE cc_start: 0.8342 (t80) cc_final: 0.8000 (t80) REVERT: K 4179 MET cc_start: 0.8498 (tmm) cc_final: 0.7493 (tmm) REVERT: K 4187 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7517 (mtt-85) REVERT: K 4191 GLU cc_start: 0.8426 (tt0) cc_final: 0.7907 (tt0) REVERT: K 4555 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.7600 (mtt180) REVERT: K 4796 MET cc_start: 0.8160 (mmt) cc_final: 0.7811 (tpp) REVERT: K 4802 TYR cc_start: 0.6930 (t80) cc_final: 0.6564 (t80) REVERT: K 4837 MET cc_start: 0.9265 (mmm) cc_final: 0.8776 (mmt) REVERT: K 4980 GLU cc_start: 0.7869 (pm20) cc_final: 0.7499 (pm20) REVERT: K 4995 ASN cc_start: 0.8624 (t0) cc_final: 0.7973 (t0) REVERT: L 1 MET cc_start: 0.7111 (mtp) cc_final: 0.6756 (mtt) outliers start: 0 outliers final: 0 residues processed: 2250 average time/residue: 0.8374 time to fit residues: 3392.8023 Evaluate side-chains 1985 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1985 time to evaluate : 8.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 950 optimal weight: 0.8980 chunk 1531 optimal weight: 0.7980 chunk 934 optimal weight: 2.9990 chunk 726 optimal weight: 2.9990 chunk 1064 optimal weight: 30.0000 chunk 1605 optimal weight: 3.9990 chunk 1478 optimal weight: 30.0000 chunk 1278 optimal weight: 0.7980 chunk 132 optimal weight: 0.0470 chunk 987 optimal weight: 5.9990 chunk 784 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 87 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 681 HIS ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1776 HIS B1862 GLN B2096 GLN ** B2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 ASN ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 87 HIS E 71 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 681 HIS ** E1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1776 HIS E1862 GLN E2096 GLN ** E2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3767 ASN ** E3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4015 GLN ** E4029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN G 87 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS H 624 ASN H 681 HIS H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2113 GLN H2261 ASN ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3767 ASN H4015 GLN H4029 ASN ** H4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN J 87 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 624 ASN K 681 HIS ** K1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1776 HIS K1862 GLN ** K2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3767 ASN ** K3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K4015 GLN ** K4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 113972 Z= 0.196 Angle : 0.581 11.690 155608 Z= 0.285 Chirality : 0.038 0.216 18776 Planarity : 0.004 0.079 20052 Dihedral : 3.969 24.232 16964 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.07), residues: 14452 helix: 2.10 (0.06), residues: 7204 sheet: -0.59 (0.14), residues: 1288 loop : -1.30 (0.08), residues: 5960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H1143 HIS 0.009 0.001 HIS E 255 PHE 0.026 0.002 PHE B2013 TYR 0.026 0.002 TYR E4168 ARG 0.009 0.001 ARG H5027 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28904 Ramachandran restraints generated. 14452 Oldfield, 0 Emsley, 14452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2216 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2210 time to evaluate : 8.888 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: B 134 ASP cc_start: 0.7749 (m-30) cc_final: 0.7333 (m-30) REVERT: B 418 LEU cc_start: 0.8511 (tt) cc_final: 0.8262 (tp) REVERT: B 634 GLN cc_start: 0.8925 (mm110) cc_final: 0.8178 (mt0) REVERT: B 710 ASP cc_start: 0.8093 (m-30) cc_final: 0.7824 (m-30) REVERT: B 735 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7018 (mm110) REVERT: B 799 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6762 (mp0) REVERT: B 847 SER cc_start: 0.7784 (t) cc_final: 0.7509 (p) REVERT: B 1081 TYR cc_start: 0.7990 (m-80) cc_final: 0.7712 (m-80) REVERT: B 1141 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7405 (ptp-170) REVERT: B 1293 LEU cc_start: 0.8472 (mp) cc_final: 0.8189 (mp) REVERT: B 1444 GLU cc_start: 0.7675 (mp0) cc_final: 0.7058 (mp0) REVERT: B 1446 SER cc_start: 0.8607 (p) cc_final: 0.8351 (m) REVERT: B 1600 LEU cc_start: 0.8014 (tp) cc_final: 0.7773 (tt) REVERT: B 1601 MET cc_start: 0.8194 (tpp) cc_final: 0.7252 (mtm) REVERT: B 1648 MET cc_start: 0.7745 (ttm) cc_final: 0.7517 (ttp) REVERT: B 1721 GLU cc_start: 0.8538 (tt0) cc_final: 0.7783 (tp30) REVERT: B 1761 HIS cc_start: 0.8364 (m-70) cc_final: 0.8152 (m90) REVERT: B 1854 ILE cc_start: 0.8964 (mm) cc_final: 0.8749 (mm) REVERT: B 1930 MET cc_start: 0.7776 (ttt) cc_final: 0.7532 (ttt) REVERT: B 1999 PHE cc_start: 0.8693 (t80) cc_final: 0.8313 (t80) REVERT: B 2009 MET cc_start: 0.7287 (ttm) cc_final: 0.6379 (tpp) REVERT: B 2146 SER cc_start: 0.7436 (p) cc_final: 0.7074 (t) REVERT: B 2171 MET cc_start: 0.7948 (tpp) cc_final: 0.7568 (tpt) REVERT: B 2212 MET cc_start: 0.7330 (tpp) cc_final: 0.6738 (tpt) REVERT: B 2229 MET cc_start: 0.8596 (tmm) cc_final: 0.7969 (tmm) REVERT: B 2239 TYR cc_start: 0.8165 (m-80) cc_final: 0.7864 (m-80) REVERT: B 2251 MET cc_start: 0.9104 (tpt) cc_final: 0.8710 (tpt) REVERT: B 2292 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7603 (mm-40) REVERT: B 2319 TYR cc_start: 0.7965 (m-80) cc_final: 0.7473 (m-10) REVERT: B 2616 ARG cc_start: 0.7011 (mtp-110) cc_final: 0.5980 (ptt180) REVERT: B 3664 SER cc_start: 0.9026 (m) cc_final: 0.8703 (t) REVERT: B 3669 MET cc_start: 0.7598 (ttt) cc_final: 0.6449 (ttp) REVERT: B 3725 MET cc_start: 0.7030 (mtm) cc_final: 0.6498 (mtm) REVERT: B 3772 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 4013 ASP cc_start: 0.8337 (m-30) cc_final: 0.8077 (m-30) REVERT: B 4029 ASN cc_start: 0.7373 (t0) cc_final: 0.7109 (t0) REVERT: B 4034 MET cc_start: 0.6013 (mtt) cc_final: 0.5411 (mmt) REVERT: B 4170 ARG cc_start: 0.8758 (tpp80) cc_final: 0.8539 (tpp80) REVERT: B 4179 MET cc_start: 0.8473 (tmm) cc_final: 0.7400 (tmm) REVERT: B 4187 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7437 (mtt-85) REVERT: B 4555 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7711 (mtt180) REVERT: B 4796 MET cc_start: 0.8048 (mmt) cc_final: 0.7723 (tpp) REVERT: B 4802 TYR cc_start: 0.6801 (t80) cc_final: 0.6484 (t80) REVERT: B 4837 MET cc_start: 0.9214 (mmm) cc_final: 0.8713 (mmt) REVERT: B 4980 GLU cc_start: 0.6438 (mp0) cc_final: 0.5872 (mp0) REVERT: B 4995 ASN cc_start: 0.8585 (t0) cc_final: 0.7979 (t0) REVERT: E 113 HIS cc_start: 0.8424 (t70) cc_final: 0.8156 (t70) REVERT: E 134 ASP cc_start: 0.7743 (m-30) cc_final: 0.7493 (m-30) REVERT: E 167 ASP cc_start: 0.9025 (m-30) cc_final: 0.8308 (p0) REVERT: E 418 LEU cc_start: 0.8488 (tt) cc_final: 0.8233 (tp) REVERT: E 710 ASP cc_start: 0.8077 (m-30) cc_final: 0.7817 (m-30) REVERT: E 735 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6962 (mm110) REVERT: E 847 SER cc_start: 0.7781 (t) cc_final: 0.7520 (p) REVERT: E 1081 TYR cc_start: 0.7978 (m-80) cc_final: 0.7721 (m-80) REVERT: E 1141 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7409 (ptp-170) REVERT: E 1293 LEU cc_start: 0.8464 (mp) cc_final: 0.8178 (mp) REVERT: E 1444 GLU cc_start: 0.7629 (mp0) cc_final: 0.7044 (mp0) REVERT: E 1446 SER cc_start: 0.8621 (p) cc_final: 0.8351 (m) REVERT: E 1601 MET cc_start: 0.8243 (tpp) cc_final: 0.7298 (mtm) REVERT: E 1648 MET cc_start: 0.7782 (ttm) cc_final: 0.7547 (ttp) REVERT: E 1761 HIS cc_start: 0.8372 (m-70) cc_final: 0.8150 (m90) REVERT: E 1854 ILE cc_start: 0.8993 (mm) cc_final: 0.8765 (mm) REVERT: E 1999 PHE cc_start: 0.8705 (t80) cc_final: 0.8306 (t80) REVERT: E 2000 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7389 (mtp85) REVERT: E 2009 MET cc_start: 0.7310 (ttm) cc_final: 0.6410 (tpp) REVERT: E 2146 SER cc_start: 0.7448 (p) cc_final: 0.7081 (t) REVERT: E 2171 MET cc_start: 0.7941 (tpp) cc_final: 0.7626 (tpt) REVERT: E 2179 MET cc_start: 0.7636 (tpp) cc_final: 0.7416 (tpp) REVERT: E 2212 MET cc_start: 0.7283 (tpp) cc_final: 0.6711 (tpt) REVERT: E 2229 MET cc_start: 0.8644 (tmm) cc_final: 0.7944 (tmm) REVERT: E 2239 TYR cc_start: 0.8198 (m-80) cc_final: 0.7870 (m-80) REVERT: E 2251 MET cc_start: 0.9272 (tpt) cc_final: 0.8874 (tpt) REVERT: E 2292 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7616 (mm-40) REVERT: E 2319 TYR cc_start: 0.7951 (m-80) cc_final: 0.7458 (m-10) REVERT: E 2616 ARG cc_start: 0.7006 (mtp-110) cc_final: 0.5981 (ptt180) REVERT: E 3664 SER cc_start: 0.9084 (m) cc_final: 0.8744 (t) REVERT: E 3725 MET cc_start: 0.6967 (mtm) cc_final: 0.6381 (mtm) REVERT: E 3772 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7981 (mm-30) REVERT: E 3777 MET cc_start: 0.8467 (tpp) cc_final: 0.8108 (mmm) REVERT: E 3846 ASN cc_start: 0.8254 (p0) cc_final: 0.7822 (m110) REVERT: E 3994 MET cc_start: 0.4995 (tpt) cc_final: 0.4382 (tpp) REVERT: E 4013 ASP cc_start: 0.8268 (m-30) cc_final: 0.8004 (m-30) REVERT: E 4034 MET cc_start: 0.6285 (mtp) cc_final: 0.5765 (mmt) REVERT: E 4136 PHE cc_start: 0.8313 (t80) cc_final: 0.8043 (t80) REVERT: E 4179 MET cc_start: 0.8517 (tmm) cc_final: 0.7390 (tmm) REVERT: E 4187 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7733 (mtt-85) REVERT: E 4191 GLU cc_start: 0.8450 (tt0) cc_final: 0.7862 (tt0) REVERT: E 4555 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7703 (mtt180) REVERT: E 4796 MET cc_start: 0.8049 (mmt) cc_final: 0.7729 (tpp) REVERT: E 4802 TYR cc_start: 0.6758 (t80) cc_final: 0.6390 (t80) REVERT: E 4837 MET cc_start: 0.9178 (mmm) cc_final: 0.8672 (mmt) REVERT: E 4980 GLU cc_start: 0.7545 (pm20) cc_final: 0.7176 (pm20) REVERT: E 4995 ASN cc_start: 0.8625 (t0) cc_final: 0.8036 (t0) REVERT: H 113 HIS cc_start: 0.8448 (t70) cc_final: 0.8177 (t70) REVERT: H 418 LEU cc_start: 0.8506 (tt) cc_final: 0.8249 (tp) REVERT: H 710 ASP cc_start: 0.8075 (m-30) cc_final: 0.7809 (m-30) REVERT: H 735 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6929 (mm110) REVERT: H 847 SER cc_start: 0.7792 (t) cc_final: 0.7531 (p) REVERT: H 1081 TYR cc_start: 0.7973 (m-80) cc_final: 0.7711 (m-80) REVERT: H 1141 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7401 (ptp-170) REVERT: H 1293 LEU cc_start: 0.8464 (mp) cc_final: 0.8190 (mp) REVERT: H 1444 GLU cc_start: 0.7642 (mp0) cc_final: 0.7047 (mp0) REVERT: H 1446 SER cc_start: 0.8610 (p) cc_final: 0.8327 (m) REVERT: H 1601 MET cc_start: 0.8237 (tpp) cc_final: 0.7292 (mtm) REVERT: H 1648 MET cc_start: 0.7797 (ttm) cc_final: 0.7558 (ttp) REVERT: H 1761 HIS cc_start: 0.8390 (m-70) cc_final: 0.8170 (m90) REVERT: H 1854 ILE cc_start: 0.8990 (mm) cc_final: 0.8760 (mm) REVERT: H 1999 PHE cc_start: 0.8716 (t80) cc_final: 0.8324 (t80) REVERT: H 2000 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7374 (mtp85) REVERT: H 2009 MET cc_start: 0.7344 (ttm) cc_final: 0.6420 (tpp) REVERT: H 2146 SER cc_start: 0.7450 (p) cc_final: 0.7089 (t) REVERT: H 2171 MET cc_start: 0.7896 (tpp) cc_final: 0.7602 (tpt) REVERT: H 2212 MET cc_start: 0.7442 (tpp) cc_final: 0.6857 (tpt) REVERT: H 2229 MET cc_start: 0.8642 (tmm) cc_final: 0.7943 (tmm) REVERT: H 2239 TYR cc_start: 0.8206 (m-80) cc_final: 0.7889 (m-80) REVERT: H 2292 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7607 (mm-40) REVERT: H 2319 TYR cc_start: 0.7952 (m-80) cc_final: 0.7463 (m-10) REVERT: H 2616 ARG cc_start: 0.7026 (mtp-110) cc_final: 0.6012 (ptt180) REVERT: H 3664 SER cc_start: 0.9090 (m) cc_final: 0.8785 (t) REVERT: H 3725 MET cc_start: 0.6980 (mtm) cc_final: 0.6411 (mtm) REVERT: H 3772 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7894 (mm-30) REVERT: H 3846 ASN cc_start: 0.8252 (p0) cc_final: 0.7835 (m110) REVERT: H 3994 MET cc_start: 0.5014 (tpt) cc_final: 0.4391 (tpp) REVERT: H 4013 ASP cc_start: 0.8270 (m-30) cc_final: 0.8011 (m-30) REVERT: H 4034 MET cc_start: 0.6306 (mtp) cc_final: 0.5375 (mmt) REVERT: H 4179 MET cc_start: 0.8520 (tmm) cc_final: 0.7345 (tmm) REVERT: H 4555 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.7697 (mtt180) REVERT: H 4796 MET cc_start: 0.8043 (mmt) cc_final: 0.7718 (tpp) REVERT: H 4802 TYR cc_start: 0.6799 (t80) cc_final: 0.6470 (t80) REVERT: H 4816 MET cc_start: 0.8249 (ppp) cc_final: 0.7972 (ppp) REVERT: H 4837 MET cc_start: 0.9212 (mmm) cc_final: 0.8717 (mmt) REVERT: H 4980 GLU cc_start: 0.7572 (pm20) cc_final: 0.7209 (pm20) REVERT: H 4995 ASN cc_start: 0.8631 (t0) cc_final: 0.8020 (t0) REVERT: I 73 MET cc_start: 0.7430 (ptp) cc_final: 0.5782 (ppp) REVERT: K 113 HIS cc_start: 0.8386 (t70) cc_final: 0.8109 (t70) REVERT: K 167 ASP cc_start: 0.8830 (m-30) cc_final: 0.8004 (p0) REVERT: K 403 MET cc_start: 0.8559 (mtm) cc_final: 0.8316 (mtm) REVERT: K 418 LEU cc_start: 0.8520 (tt) cc_final: 0.8246 (tp) REVERT: K 710 ASP cc_start: 0.8088 (m-30) cc_final: 0.7821 (m-30) REVERT: K 735 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6910 (mm110) REVERT: K 847 SER cc_start: 0.7793 (t) cc_final: 0.7531 (p) REVERT: K 1081 TYR cc_start: 0.7995 (m-80) cc_final: 0.7786 (m-80) REVERT: K 1141 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7419 (ptp-170) REVERT: K 1245 PHE cc_start: 0.8794 (m-80) cc_final: 0.8198 (m-80) REVERT: K 1293 LEU cc_start: 0.8454 (mp) cc_final: 0.8195 (mp) REVERT: K 1444 GLU cc_start: 0.7623 (mp0) cc_final: 0.7051 (mp0) REVERT: K 1446 SER cc_start: 0.8629 (p) cc_final: 0.8315 (m) REVERT: K 1601 MET cc_start: 0.8239 (tpp) cc_final: 0.7346 (mtm) REVERT: K 1761 HIS cc_start: 0.8391 (m-70) cc_final: 0.8176 (m90) REVERT: K 1854 ILE cc_start: 0.8999 (mm) cc_final: 0.8772 (mm) REVERT: K 1999 PHE cc_start: 0.8671 (t80) cc_final: 0.8302 (t80) REVERT: K 2000 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7672 (mtp85) REVERT: K 2009 MET cc_start: 0.7363 (ttm) cc_final: 0.6421 (tpp) REVERT: K 2146 SER cc_start: 0.7424 (p) cc_final: 0.7078 (t) REVERT: K 2171 MET cc_start: 0.8006 (tpp) cc_final: 0.7684 (tpt) REVERT: K 2212 MET cc_start: 0.7408 (tpp) cc_final: 0.6911 (tpt) REVERT: K 2229 MET cc_start: 0.8505 (tmm) cc_final: 0.7848 (tmm) REVERT: K 2239 TYR cc_start: 0.8196 (m-80) cc_final: 0.7859 (m-80) REVERT: K 2275 ASP cc_start: 0.7823 (t0) cc_final: 0.7585 (t0) REVERT: K 2292 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7687 (mm-40) REVERT: K 2319 TYR cc_start: 0.7963 (m-80) cc_final: 0.7476 (m-10) REVERT: K 2616 ARG cc_start: 0.6990 (mtp-110) cc_final: 0.5973 (ptt180) REVERT: K 3633 ARG cc_start: 0.7275 (tmt-80) cc_final: 0.6970 (tpt90) REVERT: K 3664 SER cc_start: 0.9072 (m) cc_final: 0.8761 (t) REVERT: K 3725 MET cc_start: 0.6995 (mtm) cc_final: 0.6417 (mtm) REVERT: K 3753 MET cc_start: 0.6669 (tpp) cc_final: 0.6238 (tpp) REVERT: K 3846 ASN cc_start: 0.8255 (p0) cc_final: 0.7829 (m110) REVERT: K 3994 MET cc_start: 0.4976 (tpt) cc_final: 0.4362 (tpp) REVERT: K 4013 ASP cc_start: 0.8274 (m-30) cc_final: 0.8010 (m-30) REVERT: K 4032 ASN cc_start: 0.6847 (m-40) cc_final: 0.6302 (t0) REVERT: K 4034 MET cc_start: 0.5622 (mtt) cc_final: 0.4858 (mmt) REVERT: K 4037 ARG cc_start: 0.6828 (mpt180) cc_final: 0.6017 (mmt90) REVERT: K 4179 MET cc_start: 0.8520 (tmm) cc_final: 0.7446 (tmm) REVERT: K 4555 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.7706 (mtt180) REVERT: K 4796 MET cc_start: 0.8053 (mmt) cc_final: 0.7727 (tpp) REVERT: K 4802 TYR cc_start: 0.6801 (t80) cc_final: 0.6474 (t80) REVERT: K 4837 MET cc_start: 0.9191 (mmm) cc_final: 0.8691 (mmt) REVERT: K 4980 GLU cc_start: 0.7490 (pm20) cc_final: 0.7164 (pm20) REVERT: K 4995 ASN cc_start: 0.8633 (t0) cc_final: 0.8016 (t0) REVERT: L 1 MET cc_start: 0.7175 (mtp) cc_final: 0.6803 (mtt) REVERT: L 73 MET cc_start: 0.7405 (ptp) cc_final: 0.5796 (ppp) outliers start: 6 outliers final: 2 residues processed: 2214 average time/residue: 0.8548 time to fit residues: 3412.3167 Evaluate side-chains 1973 residues out of total 12872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1971 time to evaluate : 8.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1612 random chunks: chunk 1015 optimal weight: 0.9980 chunk 1362 optimal weight: 5.9990 chunk 391 optimal weight: 0.0060 chunk 1179 optimal weight: 0.0020 chunk 188 optimal weight: 0.6980 chunk 355 optimal weight: 0.9980 chunk 1280 optimal weight: 9.9990 chunk 536 optimal weight: 4.9990 chunk 1315 optimal weight: 0.0000 chunk 162 optimal weight: 0.2980 chunk 235 optimal weight: 0.9980 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1776 HIS B1862 GLN B2096 GLN B2261 ASN ** B3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3767 ASN B3776 GLN ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3971 ASN B5001 HIS D 87 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 ASN E1776 HIS E1862 GLN E2096 GLN E2261 ASN ** E3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3767 ASN E3955 GLN E4015 GLN ** E4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E5001 HIS G 87 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1776 HIS H1862 GLN ** H2108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H3767 ASN H4015 GLN ** H4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H5001 HIS J 87 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 399 GLN K1776 HIS K1862 GLN K2261 ASN ** K3420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3767 ASN ** K3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3971 ASN K4015 GLN ** K4976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K5001 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.197306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.157129 restraints weight = 256946.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.157958 restraints weight = 149673.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.160264 restraints weight = 92939.119| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 113972 Z= 0.138 Angle : 0.542 11.811 155608 Z= 0.260 Chirality : 0.037 0.218 18776 Planarity : 0.004 0.067 20052 Dihedral : 3.562 21.500 16964 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.01 % Allowed : 0.14 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.07), residues: 14452 helix: 2.35 (0.06), residues: 7252 sheet: -0.37 (0.14), residues: 1288 loop : -1.12 (0.08), residues: 5912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H1143 HIS 0.006 0.001 HIS H2254 PHE 0.027 0.001 PHE E1549 TYR 0.019 0.001 TYR E4168 ARG 0.013 0.001 ARG H3979 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45852.20 seconds wall clock time: 785 minutes 42.51 seconds (47142.51 seconds total)