Starting phenix.real_space_refine on Tue Mar 26 14:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdc_21631/03_2024/6wdc_21631_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdc_21631/03_2024/6wdc_21631.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/6wdc_21631/03_2024/6wdc_21631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdc_21631/03_2024/6wdc_21631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdc_21631/03_2024/6wdc_21631_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdc_21631/03_2024/6wdc_21631_updated.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= 0.125 sd= 0.927 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4800 5.49 5 S 154 5.16 5 C 75449 2.51 5 N 27948 2.21 5 O 41798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 167": "OD1" <-> "OD2" Residue "b GLU 184": "OE1" <-> "OE2" Residue "b GLU 193": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d GLU 51": "OE1" <-> "OE2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i ASP 115": "OD1" <-> "OD2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k ASP 73": "OD1" <-> "OD2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m GLU 115": "OE1" <-> "OE2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ASP 72": "OD1" <-> "OD2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 89": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 8": "OE1" <-> "OE2" Residue "p ASP 15": "OD1" <-> "OD2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v ASP 45": "OD1" <-> "OD2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "v GLU 69": "OE1" <-> "OE2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 75": "OE1" <-> "OE2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 21": "OD1" <-> "OD2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150149 Number of models: 1 Model: "" Number of chains: 59 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 49, 'rna3p_pur': 784, 'rna3p_pyr': 616} Link IDs: {'rna2p': 139, 'rna3p': 1399} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 212, 'rna2p_pyr': 93, 'rna3p_pur': 1462, 'rna3p_pyr': 1136} Link IDs: {'rna2p': 305, 'rna3p': 2597} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "7" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 60} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 56.72, per 1000 atoms: 0.38 Number of scatterers: 150149 At special positions: 0 Unit cell: (279.93, 266.6, 245.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 4800 15.00 O 41798 8.00 N 27948 7.00 C 75449 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.35 Conformation dependent library (CDL) restraints added in 6.8 seconds 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11074 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 190 helices and 67 sheets defined 38.8% alpha, 16.3% beta 1370 base pairs and 2939 stacking pairs defined. Time for finding SS restraints: 72.01 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 7.451A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.837A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.390A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 5.631A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.444A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 201 removed outlier: 3.984A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.664A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.425A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 103' Processing helix chain 'c' and resid 120 through 125 removed outlier: 3.503A pdb=" N TRP c 125 " --> pdb=" O THR c 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.566A pdb=" N VAL d 28 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.671A pdb=" N LYS d 106 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.668A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 165 removed outlier: 3.828A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 3.811A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.557A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET d 199 " --> pdb=" O GLN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 removed outlier: 3.924A pdb=" N ASP e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 removed outlier: 4.096A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 61 removed outlier: 4.003A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 4.236A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 110 removed outlier: 4.271A pdb=" N ARG e 109 " --> pdb=" O ILE e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.426A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.237A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Proline residue: e 28 - end of helix Processing helix chain 'e' and resid 39 through 44 removed outlier: 5.413A pdb=" N ALA e 42 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA e 44 " --> pdb=" O GLU e 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 39 through 44' Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.718A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (cutoff:3.500A) Proline residue: e 138 - end of helix No H-bonds generated for 'chain 'e' and resid 133 through 138' Processing helix chain 'f' and resid 1 through 7 Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.581A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.110A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG f 152 " --> pdb=" O ARG f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 removed outlier: 3.786A pdb=" N ALA g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.566A pdb=" N ARG g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 72 removed outlier: 5.151A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA g 63 " --> pdb=" O ALA g 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA g 64 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 4.431A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 4.069A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.520A pdb=" N ASP h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE h 11 " --> pdb=" O ASP h 7 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.516A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 71 removed outlier: 4.113A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix removed outlier: 4.715A pdb=" N CYS h 71 " --> pdb=" O THR h 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 62 through 71' Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.649A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS h 105 " --> pdb=" O LYS h 101 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 77 removed outlier: 4.028A pdb=" N ALA h 75 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE h 76 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL h 77 " --> pdb=" O ASP h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 72 through 77' Processing helix chain 'h' and resid 109 through 114 removed outlier: 6.427A pdb=" N ALA h 112 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 5.072A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 46 removed outlier: 3.558A pdb=" N PHE i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.595A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY i 84 " --> pdb=" O LYS i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 113 removed outlier: 3.512A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.677A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.570A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.714A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.044A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS j 106 " --> pdb=" O GLU j 102 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY j 107 " --> pdb=" O ILE j 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.961A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 114 removed outlier: 5.858A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 109 through 114' Processing helix chain 'l' and resid 37 through 42 removed outlier: 3.825A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.925A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 86 removed outlier: 3.843A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLU l 86 " --> pdb=" O LEU l 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 99 removed outlier: 6.214A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.794A pdb=" N ARG l 132 " --> pdb=" O THR l 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 57 removed outlier: 4.174A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 124 removed outlier: 3.796A pdb=" N ALA m 113 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG m 114 " --> pdb=" O GLU m 110 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU m 115 " --> pdb=" O GLU m 111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA m 116 " --> pdb=" O LEU m 112 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE m 117 " --> pdb=" O ALA m 113 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 31 removed outlier: 3.553A pdb=" N PHE n 21 " --> pdb=" O ARG n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 3.828A pdb=" N GLU n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.916A pdb=" N LEU n 54 " --> pdb=" O PRO n 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA n 55 " --> pdb=" O LEU n 51 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.718A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG n 71 " --> pdb=" O PHE n 67 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 3.783A pdb=" N VAL n 76 " --> pdb=" O ASP n 72 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.577A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 3.997A pdb=" N ALA o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 55 through 63' Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.812A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.870A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 3.590A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 4.703A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.604A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU q 17 " --> pdb=" O HIS q 13 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA q 20 " --> pdb=" O ILE q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.013A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 53 removed outlier: 3.756A pdb=" N ARG q 49 " --> pdb=" O ALA q 45 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN q 51 " --> pdb=" O ARG q 47 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 55 through 72 removed outlier: 3.541A pdb=" N TRP q 60 " --> pdb=" O PHE q 56 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.583A pdb=" N GLY q 81 " --> pdb=" O LYS q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.554A pdb=" N LEU q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.742A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 4.243A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG s 18 " --> pdb=" O ALA s 14 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.642A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR s 39 " --> pdb=" O ILE s 35 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.871A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 4.019A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 Processing helix chain 't' and resid 39 through 51 removed outlier: 3.567A pdb=" N ILE t 43 " --> pdb=" O THR t 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.256A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 22 removed outlier: 3.851A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 4.462A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.530A pdb=" N ILE x 58 " --> pdb=" O GLY x 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.902A pdb=" N LEU x 67 " --> pdb=" O ILE x 63 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 7 removed outlier: 3.617A pdb=" N GLU y 5 " --> pdb=" O MET y 1 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.921A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.020A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN y 58 " --> pdb=" O LYS y 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA y 61 " --> pdb=" O LEU y 57 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.568A pdb=" N LYS z 20 " --> pdb=" O LEU z 16 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU z 23 " --> pdb=" O HIS z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 51 removed outlier: 4.170A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA z 49 " --> pdb=" O GLY z 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 5.099A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.643A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.605A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.759A pdb=" N GLN D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.926A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.971A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.816A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.399A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 4 through 12 removed outlier: 3.929A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 removed outlier: 4.192A pdb=" N LYS G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Proline residue: G 28 - end of helix No H-bonds generated for 'chain 'G' and resid 23 through 28' Processing helix chain 'G' and resid 41 through 63 removed outlier: 3.538A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.519A pdb=" N ASN G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.290A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 123 removed outlier: 5.331A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.543A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.682A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.875A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.519A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.542A pdb=" N ILE H 9 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 47 removed outlier: 4.655A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.572A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.685A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 5.543A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 126 removed outlier: 3.703A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.560A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.885A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.562A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.810A pdb=" N GLU I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.807A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.606A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.869A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 165 removed outlier: 4.041A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 3.606A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 191' Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.391A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.517A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.352A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 removed outlier: 4.021A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.036A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 4.061A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 18 removed outlier: 3.900A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 removed outlier: 3.583A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.505A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.651A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.775A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.959A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.568A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 removed outlier: 3.671A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.746A pdb=" N LEU M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU M 41 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.807A pdb=" N ALA M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 46 through 53 Proline residue: N 50 - end of helix removed outlier: 3.940A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 46 through 53' Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.844A pdb=" N ALA N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 5.395A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 5.653A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 3.743A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.121A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 45 through 50' Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.846A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 72 removed outlier: 3.564A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.883A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN P 100 " --> pdb=" O ILE P 96 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA P 101 " --> pdb=" O ARG P 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.811A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL Q 7 " --> pdb=" O VAL Q 3 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 26 removed outlier: 5.901A pdb=" N ALA Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.561A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.671A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.609A pdb=" N SER R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.395A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 4.073A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.596A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.685A pdb=" N LYS R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.615A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 50 removed outlier: 3.533A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.965A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.619A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.563A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 42 removed outlier: 3.588A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.723A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.568A pdb=" N THR T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.709A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.800A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.150A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 12 through 17' Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.521A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 4.059A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.901A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY X 25 " --> pdb=" O ALA X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.176A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.584A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 62 Proline residue: Y 55 - end of helix removed outlier: 3.668A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA Y 62 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.170A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN Y 83 " --> pdb=" O THR Y 79 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 3.606A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 32 removed outlier: 5.207A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.822A pdb=" N ARG Z 44 " --> pdb=" O PRO Z 40 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Z 54 " --> pdb=" O SER Z 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 5.151A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 3.641A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 59 removed outlier: 4.037A pdb=" N ASN a 58 " --> pdb=" O LYS a 54 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL a 59 " --> pdb=" O SER a 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 54 through 59' Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.501A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 36 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 72 through 78 removed outlier: 4.659A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.763A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 161 through 164 removed outlier: 6.635A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU b 175 " --> pdb=" O GLU b 179 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 7 removed outlier: 7.312A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS c 106 " --> pdb=" O ALA c 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL c 172 " --> pdb=" O VAL c 109 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 10 through 17 removed outlier: 4.438A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE c 22 " --> pdb=" O ILE c 14 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 36 through 40 removed outlier: 3.595A pdb=" N GLN c 36 " --> pdb=" O GLN c 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU c 40 " --> pdb=" O TYR c 45 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR c 45 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 46 through 51 removed outlier: 6.280A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'd' and resid 1 through 5 removed outlier: 5.346A pdb=" N MET d 1 " --> pdb=" O THR d 13 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR d 13 " --> pdb=" O MET d 1 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU d 3 " --> pdb=" O ALA d 11 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA d 11 " --> pdb=" O LEU d 3 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU d 5 " --> pdb=" O GLN d 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.631A pdb=" N MET d 188 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS d 185 " --> pdb=" O ASP d 145 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL d 146 " --> pdb=" O LYS d 166 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'e' and resid 32 through 38 Processing sheet with id= 12, first strand: chain 'e' and resid 126 through 132 Processing sheet with id= 13, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.559A pdb=" N LYS f 17 " --> pdb=" O THR f 24 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN f 21 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU f 36 " --> pdb=" O GLN f 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE f 23 " --> pdb=" O ARG f 34 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 41 through 44 Processing sheet with id= 15, first strand: chain 'f' and resid 82 through 88 removed outlier: 4.308A pdb=" N PHE f 82 " --> pdb=" O GLY f 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS f 84 " --> pdb=" O LEU f 132 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU f 132 " --> pdb=" O LYS f 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU f 86 " --> pdb=" O ILE f 130 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL f 131 " --> pdb=" O GLU f 123 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 17, first strand: chain 'g' and resid 2 through 6 removed outlier: 6.093A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA g 39 " --> pdb=" O GLN g 2 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 76 through 83 removed outlier: 6.362A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN g 145 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'h' and resid 23 through 28 removed outlier: 4.204A pdb=" N LEU h 23 " --> pdb=" O GLU h 87 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL h 27 " --> pdb=" O ALA h 83 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'j' and resid 52 through 57 removed outlier: 4.822A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'j' and resid 74 through 77 Processing sheet with id= 22, first strand: chain 'k' and resid 6 through 10 removed outlier: 6.491A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'l' and resid 88 through 91 Processing sheet with id= 24, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.507A pdb=" N GLU m 104 " --> pdb=" O TRP m 64 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'm' and resid 99 through 102 removed outlier: 3.636A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.925A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.529A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS o 29 " --> pdb=" O TYR o 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN o 38 " --> pdb=" O VAL o 27 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL o 27 " --> pdb=" O GLN o 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU o 26 " --> pdb=" O SER o 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP o 93 " --> pdb=" O LEU o 26 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.158A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'p' and resid 48 through 52 removed outlier: 4.378A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.819A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR r 2 " --> pdb=" O ALA r 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.650A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER r 102 " --> pdb=" O VAL r 58 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'r' and resid 65 through 73 removed outlier: 3.768A pdb=" N ALA r 65 " --> pdb=" O ASP r 95 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS r 73 " --> pdb=" O GLN r 87 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN r 87 " --> pdb=" O LYS r 73 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 's' and resid 2 through 8 removed outlier: 4.450A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL s 105 " --> pdb=" O ALA s 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 't' and resid 12 through 15 removed outlier: 5.415A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL t 85 " --> pdb=" O ILE t 30 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU t 32 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.027A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'u' and resid 81 through 86 removed outlier: 5.481A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'v' and resid 2 through 5 Processing sheet with id= 38, first strand: chain 'v' and resid 37 through 41 removed outlier: 4.404A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 47 through 50 removed outlier: 6.345A pdb=" N GLY w 48 " --> pdb=" O LEU w 55 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU w 55 " --> pdb=" O GLY w 48 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY w 50 " --> pdb=" O HIS w 53 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'w' and resid 62 through 68 removed outlier: 3.754A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER w 77 " --> pdb=" O LYS w 64 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'x' and resid 11 through 15 Processing sheet with id= 42, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.605A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 27 through 30 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'C' and resid 7 through 11 Processing sheet with id= 45, first strand: chain 'C' and resid 33 through 36 removed outlier: 7.539A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 14 through 17 removed outlier: 5.536A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 66 through 70 Processing sheet with id= 48, first strand: chain 'H' and resid 52 through 58 removed outlier: 3.779A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 65 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.633A pdb=" N VAL H 152 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE H 201 " --> pdb=" O ASP H 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP H 182 " --> pdb=" O ILE H 201 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 139 through 143 removed outlier: 3.521A pdb=" N ASP I 140 " --> pdb=" O PHE I 181 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 12 through 15 removed outlier: 7.259A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 92 through 97 removed outlier: 4.049A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN J 96 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 31 through 39 removed outlier: 4.672A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 58 through 65 removed outlier: 3.594A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET K 9 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARG K 86 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'L' and resid 72 through 78 No H-bonds generated for sheet with id= 55 Processing sheet with id= 56, first strand: chain 'M' and resid 23 through 26 removed outlier: 3.788A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET M 26 " --> pdb=" O LEU M 58 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 73 through 76 removed outlier: 4.731A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'N' and resid 14 through 21 removed outlier: 3.542A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'O' and resid 40 through 52 removed outlier: 6.240A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'P' and resid 29 through 33 removed outlier: 3.583A pdb=" N GLY P 18 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU P 82 " --> pdb=" O GLY P 18 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 28 through 32 Processing sheet with id= 62, first strand: chain 'Q' and resid 34 through 40 removed outlier: 5.013A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 2 through 10 removed outlier: 3.502A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 38 through 46 removed outlier: 7.037A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU V 25 " --> pdb=" O GLN V 8 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLN V 8 " --> pdb=" O GLU V 25 " (cutoff:3.500A) removed outlier: 13.767A pdb=" N PHE V 27 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 16.607A pdb=" N THR V 6 " --> pdb=" O PHE V 27 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP V 56 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'X' and resid 29 through 33 removed outlier: 4.009A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL X 59 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'a' and resid 60 through 64 Processing sheet with id= 67, first strand: chain 'a' and resid 169 through 176 removed outlier: 6.206A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) 1494 hydrogen bonds defined for protein. 4422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3386 hydrogen bonds 5648 hydrogen bond angles 0 basepair planarities 1370 basepair parallelities 2939 stacking parallelities Total time for adding SS restraints: 264.60 Time building geometry restraints manager: 67.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 34506 1.34 - 1.47: 66299 1.47 - 1.60: 56913 1.60 - 1.72: 5143 1.72 - 1.85: 278 Bond restraints: 163139 Sorted by residual: bond pdb=" CA THR K 97 " pdb=" CB THR K 97 " ideal model delta sigma weight residual 1.527 1.549 -0.021 7.60e-03 1.73e+04 7.85e+00 bond pdb=" CA PRO i 21 " pdb=" C PRO i 21 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.10e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.42e+00 bond pdb=" N GLY a 159 " pdb=" CA GLY a 159 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.48e+00 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.35e+00 ... (remaining 163134 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.08: 27512 106.08 - 113.07: 92578 113.07 - 120.06: 62371 120.06 - 127.05: 49602 127.05 - 134.04: 12019 Bond angle restraints: 244082 Sorted by residual: angle pdb=" N VAL n 116 " pdb=" CA VAL n 116 " pdb=" C VAL n 116 " ideal model delta sigma weight residual 106.21 118.16 -11.95 1.07e+00 8.73e-01 1.25e+02 angle pdb=" N VAL Q 20 " pdb=" CA VAL Q 20 " pdb=" C VAL Q 20 " ideal model delta sigma weight residual 107.89 119.78 -11.89 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N THR D 4 " pdb=" CA THR D 4 " pdb=" C THR D 4 " ideal model delta sigma weight residual 112.93 124.39 -11.46 1.12e+00 7.97e-01 1.05e+02 angle pdb=" N LYS a 31 " pdb=" CA LYS a 31 " pdb=" C LYS a 31 " ideal model delta sigma weight residual 113.28 101.18 12.10 1.22e+00 6.72e-01 9.84e+01 angle pdb=" N SER b 87 " pdb=" CA SER b 87 " pdb=" C SER b 87 " ideal model delta sigma weight residual 113.50 102.06 11.44 1.23e+00 6.61e-01 8.65e+01 ... (remaining 244077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 93635 35.89 - 71.79: 9730 71.79 - 107.68: 1207 107.68 - 143.57: 8 143.57 - 179.46: 19 Dihedral angle restraints: 104599 sinusoidal: 87439 harmonic: 17160 Sorted by residual: dihedral pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " pdb=" C1' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 31.96 -66.96 1 8.00e+00 1.56e-02 9.13e+01 dihedral pdb=" O4' G 12286 " pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " ideal model delta sinusoidal sigma weight residual 24.00 -41.25 65.25 1 8.00e+00 1.56e-02 8.72e+01 dihedral pdb=" O4' C 2 12 " pdb=" C1' C 2 12 " pdb=" N1 C 2 12 " pdb=" C2 C 2 12 " ideal model delta sinusoidal sigma weight residual 200.00 34.52 165.48 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 104596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 22293 0.094 - 0.188: 8291 0.188 - 0.281: 581 0.281 - 0.375: 48 0.375 - 0.469: 7 Chirality restraints: 31220 Sorted by residual: chirality pdb=" CA ASN Z 8 " pdb=" N ASN Z 8 " pdb=" C ASN Z 8 " pdb=" CB ASN Z 8 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA MET b 131 " pdb=" N MET b 131 " pdb=" C MET b 131 " pdb=" CB MET b 131 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA THR D 4 " pdb=" N THR D 4 " pdb=" C THR D 4 " pdb=" CB THR D 4 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 31217 not shown) Planarity restraints: 13080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12629 " 0.079 2.00e-02 2.50e+03 4.39e-02 4.33e+01 pdb=" N1 U 12629 " -0.003 2.00e-02 2.50e+03 pdb=" C2 U 12629 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U 12629 " -0.029 2.00e-02 2.50e+03 pdb=" N3 U 12629 " -0.016 2.00e-02 2.50e+03 pdb=" C4 U 12629 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U 12629 " 0.079 2.00e-02 2.50e+03 pdb=" C5 U 12629 " -0.042 2.00e-02 2.50e+03 pdb=" C6 U 12629 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 3 244 " 0.069 2.00e-02 2.50e+03 4.07e-02 3.73e+01 pdb=" N1 U 3 244 " 0.001 2.00e-02 2.50e+03 pdb=" C2 U 3 244 " -0.013 2.00e-02 2.50e+03 pdb=" O2 U 3 244 " -0.025 2.00e-02 2.50e+03 pdb=" N3 U 3 244 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 3 244 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U 3 244 " 0.078 2.00e-02 2.50e+03 pdb=" C5 U 3 244 " -0.042 2.00e-02 2.50e+03 pdb=" C6 U 3 244 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.069 2.00e-02 2.50e+03 4.04e-02 3.66e+01 pdb=" N1 U 11647 " 0.000 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.025 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.019 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.076 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.041 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.030 2.00e-02 2.50e+03 ... (remaining 13077 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 30046 2.79 - 3.32: 129814 3.32 - 3.84: 298654 3.84 - 4.37: 371207 4.37 - 4.90: 495427 Nonbonded interactions: 1325148 Sorted by model distance: nonbonded pdb=" O LEU s 33 " pdb=" OG1 THR s 37 " model vdw 2.262 2.440 nonbonded pdb=" O2' U 11130 " pdb=" OP1 G 11131 " model vdw 2.291 2.440 nonbonded pdb=" O ARG J 92 " pdb=" O VAL J 93 " model vdw 2.307 3.040 nonbonded pdb=" O THR D 4 " pdb=" OG1 THR D 4 " model vdw 2.310 2.440 nonbonded pdb=" OG SER N 72 " pdb=" OP2 G 31373 " model vdw 2.312 2.440 ... (remaining 1325143 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 '5' and resid 1 through 76) selection = chain '6' } 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=0.52 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: 1.890 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: 0.150 Extract box with map and model: 11.150 Check model and map are aligned: 1.590 Set scattering table: 1.120 Process input model: 562.050 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.540 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: 0.030 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 584.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.006 0.041 163139 Z= 0.350 Angle : 1.011 14.558 244082 Z= 0.665 Chirality : 0.083 0.469 31220 Planarity : 0.007 0.101 13080 Dihedral : 22.002 179.465 93525 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 2.11 % Allowed : 13.26 % Favored : 84.63 % Rotamer: Outliers : 1.14 % Allowed : 8.56 % Favored : 90.30 % 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: -5.10 (0.08), residues: 5919 helix: -3.82 (0.07), residues: 1695 sheet: -2.83 (0.15), residues: 868 loop : -3.40 (0.09), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP b 212 HIS 0.002 0.000 HIS V 46 PHE 0.036 0.005 PHE m 9 TYR 0.048 0.007 TYR G 21 ARG 0.009 0.001 ARG N 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1839 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1783 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 152 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7598 (mm-40) REVERT: b 200 MET cc_start: 0.8053 (ptt) cc_final: 0.7808 (tmm) REVERT: b 212 TRP cc_start: 0.7725 (p90) cc_final: 0.7378 (p90) REVERT: b 257 ARG cc_start: 0.6204 (tpt170) cc_final: 0.5956 (tpt170) REVERT: c 8 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8227 (ttpp) REVERT: c 28 GLU cc_start: 0.6267 (tm-30) cc_final: 0.5194 (tm-30) REVERT: c 84 LEU cc_start: 0.8368 (mt) cc_final: 0.8137 (mp) REVERT: c 136 ASN cc_start: 0.8057 (t0) cc_final: 0.7588 (t0) REVERT: c 154 LYS cc_start: 0.7288 (pttp) cc_final: 0.7051 (pttm) REVERT: c 157 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7868 (mtpp) REVERT: d 156 ASN cc_start: 0.8792 (m-40) cc_final: 0.8097 (t0) REVERT: d 166 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8112 (mtpp) REVERT: e 19 PHE cc_start: 0.8026 (m-80) cc_final: 0.7762 (m-80) REVERT: e 37 MET cc_start: 0.9401 (tpt) cc_final: 0.9191 (tpp) REVERT: e 56 LEU cc_start: 0.8969 (tp) cc_final: 0.8683 (tp) REVERT: e 82 TYR cc_start: 0.7561 (t80) cc_final: 0.7028 (t80) REVERT: e 163 GLU cc_start: 0.9265 (pp20) cc_final: 0.8770 (pm20) REVERT: e 164 GLU cc_start: 0.8643 (tp30) cc_final: 0.8437 (tp30) REVERT: f 36 LEU cc_start: 0.7363 (mt) cc_final: 0.6833 (pp) REVERT: f 41 GLU cc_start: 0.8885 (tt0) cc_final: 0.8421 (tp30) REVERT: f 94 ARG cc_start: 0.6989 (mmt-90) cc_final: 0.6347 (mmp80) REVERT: f 103 ASN cc_start: 0.8661 (t0) cc_final: 0.8412 (t0) REVERT: f 127 GLN cc_start: 0.7621 (mm110) cc_final: 0.7224 (mm110) REVERT: g 15 LEU cc_start: 0.9412 (mt) cc_final: 0.9204 (mt) REVERT: h 1 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.2688 (ppp) REVERT: h 38 MET cc_start: 0.6954 (mmt) cc_final: 0.6651 (mmt) REVERT: h 86 MET cc_start: 0.3391 (tpp) cc_final: 0.3039 (tpt) REVERT: i 116 MET cc_start: -0.0691 (ttt) cc_final: -0.1041 (ttt) REVERT: j 31 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7084 (mm-30) REVERT: j 41 LYS cc_start: 0.8901 (mttt) cc_final: 0.8441 (mttt) REVERT: j 53 TYR cc_start: 0.7277 (m-80) cc_final: 0.6995 (m-10) REVERT: j 95 ARG cc_start: 0.8180 (mpt180) cc_final: 0.7946 (mmt180) REVERT: j 106 LYS cc_start: 0.8033 (tptt) cc_final: 0.7718 (tptt) REVERT: j 118 MET cc_start: 0.8997 (ptp) cc_final: 0.8628 (ptp) REVERT: j 136 GLN cc_start: 0.7528 (mt0) cc_final: 0.7204 (mp10) REVERT: k 2 ILE cc_start: 0.8521 (mm) cc_final: 0.8174 (mm) REVERT: k 86 LEU cc_start: 0.8976 (mt) cc_final: 0.8730 (mp) REVERT: l 55 MET cc_start: 0.8347 (mmp) cc_final: 0.8122 (mmt) REVERT: m 12 MET cc_start: 0.5034 (mtp) cc_final: 0.4828 (mmm) REVERT: m 62 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7631 (tttm) REVERT: m 111 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7826 (mm-30) REVERT: n 17 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: n 69 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8109 (mmt90) REVERT: n 73 ASN cc_start: 0.8417 (m-40) cc_final: 0.7820 (m-40) REVERT: o 8 ILE cc_start: 0.9212 (mm) cc_final: 0.8994 (mp) REVERT: o 17 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8282 (mmtp) REVERT: p 43 GLU cc_start: 0.7105 (tp30) cc_final: 0.6359 (tp30) REVERT: p 102 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.6806 (mtt90) REVERT: p 114 ASN cc_start: 0.8182 (p0) cc_final: 0.7549 (m110) REVERT: q 17 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8815 (mp) REVERT: q 53 LYS cc_start: 0.7806 (mttp) cc_final: 0.7482 (mmtt) REVERT: q 75 TYR cc_start: 0.8245 (t80) cc_final: 0.7065 (t80) REVERT: q 93 ILE cc_start: 0.8531 (mm) cc_final: 0.8148 (mm) REVERT: r 13 ARG cc_start: 0.8605 (ttt-90) cc_final: 0.8038 (ttt-90) REVERT: r 22 LEU cc_start: 0.6798 (pp) cc_final: 0.6440 (pp) REVERT: r 49 ILE cc_start: 0.5333 (pt) cc_final: 0.5122 (pt) REVERT: r 71 LYS cc_start: 0.7607 (ttmm) cc_final: 0.7143 (tppt) REVERT: r 89 HIS cc_start: 0.7769 (t-90) cc_final: 0.7488 (t70) REVERT: s 6 LYS cc_start: 0.8657 (ptpt) cc_final: 0.8061 (ptpp) REVERT: s 15 GLN cc_start: 0.7690 (tt0) cc_final: 0.7333 (tt0) REVERT: s 18 ARG cc_start: 0.7296 (mtt180) cc_final: 0.7062 (mtt180) REVERT: s 68 ASP cc_start: 0.8789 (t0) cc_final: 0.8376 (t70) REVERT: t 11 LEU cc_start: 0.8064 (mp) cc_final: 0.7461 (mt) REVERT: t 24 MET cc_start: 0.7574 (tpp) cc_final: 0.7298 (tpp) REVERT: t 37 ASP cc_start: 0.7347 (p0) cc_final: 0.7027 (p0) REVERT: u 39 ASN cc_start: 0.8634 (m-40) cc_final: 0.8415 (m110) REVERT: u 61 GLU cc_start: 0.5270 (mp0) cc_final: 0.4891 (mp0) REVERT: u 65 GLN cc_start: 0.8695 (mp10) cc_final: 0.8143 (mp10) REVERT: u 68 ASN cc_start: 0.7710 (m110) cc_final: 0.6752 (m110) REVERT: u 73 ASN cc_start: 0.7226 (t0) cc_final: 0.6943 (t0) REVERT: v 50 MET cc_start: 0.9010 (mtp) cc_final: 0.8692 (mtp) REVERT: v 76 ASP cc_start: 0.7524 (m-30) cc_final: 0.7319 (m-30) REVERT: v 89 ILE cc_start: 0.6845 (tt) cc_final: 0.6633 (tt) REVERT: w 16 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7848 (mmt-90) REVERT: w 21 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.8083 (mmm-85) REVERT: w 22 PHE cc_start: 0.7400 (m-80) cc_final: 0.7050 (m-80) REVERT: w 60 ASP cc_start: 0.8871 (t0) cc_final: 0.8619 (t0) REVERT: x 31 ASN cc_start: 0.8389 (t0) cc_final: 0.7918 (t0) REVERT: y 13 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8694 (tp30) REVERT: y 26 PHE cc_start: 0.8774 (t80) cc_final: 0.8127 (t80) REVERT: z 10 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7359 (mpt-90) REVERT: B 35 GLU cc_start: 0.6957 (mt-10) cc_final: 0.5113 (mt-10) REVERT: B 45 ASP cc_start: 0.8126 (m-30) cc_final: 0.7754 (p0) REVERT: C 18 HIS cc_start: 0.6400 (t-90) cc_final: 0.5987 (t70) REVERT: E 61 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7374 (pp) REVERT: F 1 MET cc_start: 0.7494 (ptp) cc_final: 0.7098 (ptm) REVERT: F 34 LYS cc_start: 0.8195 (mttt) cc_final: 0.7795 (mtpt) REVERT: F 35 GLN cc_start: 0.7276 (pt0) cc_final: 0.6678 (pm20) REVERT: G 22 TRP cc_start: 0.6604 (p-90) cc_final: 0.6378 (p-90) REVERT: G 26 MET cc_start: 0.6310 (mmt) cc_final: 0.5367 (mmt) REVERT: G 34 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8394 (tpp80) REVERT: G 57 ASN cc_start: 0.8760 (t0) cc_final: 0.8424 (m-40) REVERT: G 68 PHE cc_start: 0.7049 (m-80) cc_final: 0.6635 (m-80) REVERT: G 77 GLU cc_start: 0.8217 (pm20) cc_final: 0.7906 (pm20) REVERT: G 89 PHE cc_start: 0.6612 (m-80) cc_final: 0.5840 (m-80) REVERT: G 117 GLU cc_start: 0.4991 (mt-10) cc_final: 0.4721 (mm-30) REVERT: G 121 GLN cc_start: 0.9325 (mm-40) cc_final: 0.9007 (mm-40) REVERT: G 138 ARG cc_start: 0.6875 (ptt180) cc_final: 0.6549 (ptt-90) REVERT: G 139 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: G 151 LYS cc_start: 0.8595 (tptm) cc_final: 0.8281 (mmmt) REVERT: G 176 ASN cc_start: 0.8599 (m110) cc_final: 0.8384 (t0) REVERT: G 212 TYR cc_start: 0.8623 (m-80) cc_final: 0.8251 (m-80) REVERT: H 129 PHE cc_start: 0.7606 (p90) cc_final: 0.7384 (p90) REVERT: H 135 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8233 (mtp-110) REVERT: H 138 GLN cc_start: 0.8856 (mt0) cc_final: 0.8596 (mt0) REVERT: H 156 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6859 (pp) REVERT: H 167 TYR cc_start: 0.5546 (t80) cc_final: 0.5289 (t80) REVERT: H 169 GLU cc_start: 0.7738 (tp30) cc_final: 0.7142 (tm-30) REVERT: I 104 MET cc_start: 0.3295 (mmt) cc_final: 0.3023 (mmm) REVERT: J 11 GLN cc_start: 0.7752 (tt0) cc_final: 0.7431 (mp10) REVERT: J 47 PHE cc_start: 0.8780 (p90) cc_final: 0.8361 (p90) REVERT: J 64 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8283 (mt-10) REVERT: J 88 HIS cc_start: 0.8788 (t-90) cc_final: 0.8517 (t-90) REVERT: J 110 MET cc_start: 0.8136 (ptp) cc_final: 0.7709 (ptp) REVERT: J 134 ASN cc_start: 0.6080 (t0) cc_final: 0.5445 (t0) REVERT: J 151 MET cc_start: 0.7863 (mmp) cc_final: 0.7404 (mmp) REVERT: K 13 ASP cc_start: 0.9230 (m-30) cc_final: 0.8298 (t70) REVERT: K 21 MET cc_start: 0.8445 (mtp) cc_final: 0.7931 (mtt) REVERT: K 40 GLU cc_start: 0.7344 (tt0) cc_final: 0.6757 (tp30) REVERT: K 72 ASP cc_start: 0.8979 (m-30) cc_final: 0.8692 (p0) REVERT: K 89 VAL cc_start: 0.6650 (t) cc_final: 0.6449 (m) REVERT: L 47 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8664 (tm-30) REVERT: L 48 THR cc_start: 0.8954 (p) cc_final: 0.8660 (p) REVERT: L 49 LEU cc_start: 0.9240 (pp) cc_final: 0.8937 (mm) REVERT: L 69 ARG cc_start: 0.6894 (ttm170) cc_final: 0.6683 (ttp80) REVERT: L 121 ASN cc_start: 0.9326 (m110) cc_final: 0.9010 (m-40) REVERT: L 145 GLU cc_start: 0.8128 (tp30) cc_final: 0.6724 (mp0) REVERT: M 8 ASP cc_start: 0.8404 (m-30) cc_final: 0.7832 (m-30) REVERT: M 9 MET cc_start: 0.6635 (ttp) cc_final: 0.5206 (tmm) REVERT: M 46 GLU cc_start: 0.7161 (tp30) cc_final: 0.6760 (tp30) REVERT: M 57 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7097 (mp0) REVERT: M 95 MET cc_start: 0.7346 (ttm) cc_final: 0.6953 (ttm) REVERT: M 98 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7858 (pp) REVERT: M 100 ILE cc_start: 0.8814 (pt) cc_final: 0.8541 (mm) REVERT: M 110 MET cc_start: 0.7053 (ptt) cc_final: 0.6160 (ptt) REVERT: N 11 ARG cc_start: 0.7913 (ttp80) cc_final: 0.6947 (tmm160) REVERT: N 67 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7331 (tptp) REVERT: N 74 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8373 (mm110) REVERT: N 94 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7671 (ttt-90) REVERT: N 112 ARG cc_start: 0.6456 (ptm-80) cc_final: 0.6173 (ptm-80) REVERT: N 114 LYS cc_start: 0.6748 (mppt) cc_final: 0.6249 (mtpt) REVERT: O 63 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5049 (t0) REVERT: O 66 GLU cc_start: 0.8383 (pt0) cc_final: 0.8175 (tm-30) REVERT: O 72 ARG cc_start: 0.7272 (mmt-90) cc_final: 0.6337 (mmm-85) REVERT: P 26 PHE cc_start: 0.8298 (m-80) cc_final: 0.8094 (m-80) REVERT: P 52 ARG cc_start: 0.6898 (tpp-160) cc_final: 0.5195 (ptm160) REVERT: P 118 ASN cc_start: 0.7657 (t0) cc_final: 0.6667 (p0) REVERT: Q 9 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8288 (ttpp) REVERT: Q 27 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7693 (Cg_endo) REVERT: Q 53 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7266 (tpt170) REVERT: Q 71 HIS cc_start: 0.7377 (p90) cc_final: 0.6988 (p90) REVERT: R 70 ARG cc_start: 0.9188 (mtt180) cc_final: 0.8376 (mtt180) REVERT: R 72 ILE cc_start: 0.9259 (tp) cc_final: 0.9021 (tp) REVERT: R 74 MET cc_start: 0.7732 (ppp) cc_final: 0.7469 (ppp) REVERT: R 112 ARG cc_start: 0.6710 (ttm170) cc_final: 0.5552 (ptt-90) REVERT: S 61 ASN cc_start: 0.8385 (t0) cc_final: 0.8118 (t0) REVERT: T 14 PHE cc_start: 0.8778 (m-80) cc_final: 0.8406 (m-80) REVERT: T 80 LEU cc_start: 0.8818 (mt) cc_final: 0.8371 (mt) REVERT: U 26 ASN cc_start: 0.5591 (m110) cc_final: 0.5105 (m-40) REVERT: U 32 PHE cc_start: 0.8491 (p90) cc_final: 0.8209 (p90) REVERT: U 79 ASN cc_start: 0.8236 (p0) cc_final: 0.7910 (p0) REVERT: V 62 GLU cc_start: 0.7179 (tp30) cc_final: 0.6887 (tp30) REVERT: V 79 GLU cc_start: 0.7861 (mp0) cc_final: 0.7166 (tt0) REVERT: W 29 LYS cc_start: 0.8753 (pptt) cc_final: 0.8467 (pptt) REVERT: W 51 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8548 (tm-30) REVERT: W 63 TYR cc_start: 0.8084 (t80) cc_final: 0.7560 (t80) REVERT: X 2 ARG cc_start: 0.5678 (mtm180) cc_final: 0.5157 (mtm-85) REVERT: X 28 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (tppt) REVERT: X 80 ARG cc_start: 0.4535 (mtt180) cc_final: 0.4294 (mtt180) REVERT: Y 15 LYS cc_start: 0.9356 (tppt) cc_final: 0.8980 (tppt) REVERT: Y 26 MET cc_start: 0.8255 (ppp) cc_final: 0.8044 (ppp) REVERT: Y 30 PHE cc_start: 0.8979 (m-10) cc_final: 0.8648 (m-80) REVERT: Y 34 VAL cc_start: 0.9013 (t) cc_final: 0.8526 (t) REVERT: Y 42 ASP cc_start: 0.8903 (t0) cc_final: 0.8574 (t0) REVERT: Y 50 PHE cc_start: 0.8892 (t80) cc_final: 0.8433 (t80) REVERT: Y 52 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8865 (tm-30) REVERT: Y 53 MET cc_start: 0.9048 (ptt) cc_final: 0.8828 (ptt) REVERT: Y 63 LYS cc_start: 0.7872 (mmpt) cc_final: 0.6585 (mmpt) REVERT: Y 69 ASN cc_start: 0.8039 (t0) cc_final: 0.7774 (p0) REVERT: Y 78 LEU cc_start: 0.8759 (mm) cc_final: 0.8506 (mm) REVERT: Z 46 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6824 (ptp-110) REVERT: a 4 LEU cc_start: 0.1894 (OUTLIER) cc_final: 0.1638 (tt) REVERT: a 7 ARG cc_start: 0.6695 (tpt90) cc_final: 0.6070 (mtt180) REVERT: a 167 LYS cc_start: 0.8693 (mttt) cc_final: 0.8374 (mmtt) outliers start: 56 outliers final: 15 residues processed: 1819 average time/residue: 1.4667 time to fit residues: 4438.3788 Evaluate side-chains 1386 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1362 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 20.0000 chunk 801 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 273 optimal weight: 0.5980 chunk 540 optimal weight: 6.9990 chunk 428 optimal weight: 8.9990 chunk 828 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 503 optimal weight: 6.9990 chunk 616 optimal weight: 20.0000 chunk 959 optimal weight: 10.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 20 ASN b 45 ASN ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN b 152 GLN ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS c 140 HIS c 148 GLN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN d 97 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 ASN f 29 ASN f 44 HIS f 47 ASN f 127 GLN g 28 ASN g 43 ASN g 66 ASN ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 ASN h 103 ASN i 30 GLN i 42 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN m 22 GLN n 3 HIS n 9 GLN ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN p 2 ASN q 36 GLN q 55 GLN q 71 ASN r 18 GLN r 87 GLN r 89 HIS ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS s 31 GLN ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** v 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 53 HIS x 5 GLN y 20 ASN y 27 ASN C 25 ASN C 44 GLN C 45 HIS D 6 GLN D 16 HIS F 35 GLN G 17 HIS G 18 GLN G 38 HIS G 50 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN I 197 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 68 GLN L 67 ASN L 121 ASN L 129 ASN N 36 GLN N 109 GLN N 125 GLN O 56 HIS ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN T 27 GLN T 50 HIS ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 HIS U 18 GLN U 26 ASN U 29 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Y 51 ASN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 163139 Z= 0.329 Angle : 0.829 15.422 244082 Z= 0.424 Chirality : 0.044 0.411 31220 Planarity : 0.007 0.101 13080 Dihedral : 22.978 179.977 81722 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.80 % Favored : 89.04 % Rotamer: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.09), residues: 5919 helix: -2.18 (0.10), residues: 1755 sheet: -2.46 (0.16), residues: 893 loop : -3.01 (0.09), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP b 212 HIS 0.009 0.002 HIS X 68 PHE 0.050 0.003 PHE g 46 TYR 0.039 0.003 TYR e 6 ARG 0.019 0.001 ARG Y 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1580 time to evaluate : 6.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 47 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7359 (ttm170) REVERT: b 160 TYR cc_start: 0.7578 (p90) cc_final: 0.7235 (p90) REVERT: b 200 MET cc_start: 0.8266 (ptt) cc_final: 0.7956 (ppp) REVERT: b 201 LEU cc_start: 0.8566 (mt) cc_final: 0.8311 (mt) REVERT: b 257 ARG cc_start: 0.6560 (tpt170) cc_final: 0.6114 (tpt170) REVERT: c 8 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8200 (ptmt) REVERT: c 35 THR cc_start: 0.9292 (p) cc_final: 0.9074 (t) REVERT: c 82 PHE cc_start: 0.7780 (m-80) cc_final: 0.7566 (m-10) REVERT: c 136 ASN cc_start: 0.8293 (t0) cc_final: 0.7923 (t0) REVERT: c 183 GLU cc_start: 0.9295 (mp0) cc_final: 0.9059 (mp0) REVERT: c 187 LEU cc_start: 0.8956 (mm) cc_final: 0.8688 (mm) REVERT: c 188 LEU cc_start: 0.8356 (mp) cc_final: 0.7792 (mp) REVERT: d 25 GLU cc_start: 0.7407 (tt0) cc_final: 0.7010 (tt0) REVERT: d 74 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8166 (ttmt) REVERT: d 106 LYS cc_start: 0.7547 (mtpt) cc_final: 0.7276 (mttm) REVERT: d 136 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7844 (tp-100) REVERT: d 140 ASP cc_start: 0.7665 (m-30) cc_final: 0.7210 (m-30) REVERT: d 156 ASN cc_start: 0.8843 (m-40) cc_final: 0.8362 (t0) REVERT: d 184 ASP cc_start: 0.7652 (m-30) cc_final: 0.7435 (m-30) REVERT: d 188 MET cc_start: 0.5818 (ptp) cc_final: 0.5559 (ptm) REVERT: d 194 LYS cc_start: 0.9484 (mmpt) cc_final: 0.9245 (mmmt) REVERT: e 19 PHE cc_start: 0.7762 (m-80) cc_final: 0.7431 (m-80) REVERT: e 51 ASN cc_start: 0.7135 (t0) cc_final: 0.6762 (t0) REVERT: e 82 TYR cc_start: 0.7687 (t80) cc_final: 0.6840 (t80) REVERT: e 88 VAL cc_start: 0.8755 (t) cc_final: 0.8479 (t) REVERT: f 41 GLU cc_start: 0.8814 (tt0) cc_final: 0.8553 (tm-30) REVERT: f 94 ARG cc_start: 0.6593 (mmt-90) cc_final: 0.6133 (mmp80) REVERT: f 103 ASN cc_start: 0.8677 (t0) cc_final: 0.8473 (t0) REVERT: f 127 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7063 (mm-40) REVERT: f 151 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7465 (mmm160) REVERT: g 7 ASP cc_start: 0.6397 (p0) cc_final: 0.6113 (p0) REVERT: g 43 ASN cc_start: 0.8275 (m110) cc_final: 0.7776 (m110) REVERT: h 1 MET cc_start: 0.3442 (ttp) cc_final: 0.2670 (ppp) REVERT: i 116 MET cc_start: -0.0248 (ttt) cc_final: -0.0472 (ttt) REVERT: j 14 ASP cc_start: 0.7582 (m-30) cc_final: 0.7261 (m-30) REVERT: j 31 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7164 (mm-30) REVERT: j 41 LYS cc_start: 0.8983 (mttt) cc_final: 0.8606 (mttt) REVERT: j 60 ASP cc_start: 0.7870 (m-30) cc_final: 0.7645 (p0) REVERT: j 118 MET cc_start: 0.8897 (ptp) cc_final: 0.8666 (ptp) REVERT: j 136 GLN cc_start: 0.7461 (mt0) cc_final: 0.6794 (mp10) REVERT: k 1 MET cc_start: 0.7304 (mtt) cc_final: 0.6884 (mtp) REVERT: k 29 HIS cc_start: 0.8410 (t70) cc_final: 0.7996 (t70) REVERT: k 80 ASP cc_start: 0.8664 (m-30) cc_final: 0.8239 (m-30) REVERT: k 98 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7639 (ttp-110) REVERT: l 59 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7120 (mtp85) REVERT: l 84 LYS cc_start: 0.8527 (mttt) cc_final: 0.8280 (mttt) REVERT: m 33 LEU cc_start: 0.6586 (tp) cc_final: 0.6174 (tt) REVERT: m 53 MET cc_start: 0.6723 (ttm) cc_final: 0.5682 (tmm) REVERT: n 17 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8260 (ttp-110) REVERT: n 64 ARG cc_start: 0.7324 (mtt180) cc_final: 0.7041 (mmt90) REVERT: n 73 ASN cc_start: 0.8498 (m-40) cc_final: 0.7813 (m-40) REVERT: o 18 LEU cc_start: 0.8539 (pt) cc_final: 0.8332 (pt) REVERT: o 38 GLN cc_start: 0.7768 (pt0) cc_final: 0.6602 (pm20) REVERT: o 92 PHE cc_start: 0.7590 (t80) cc_final: 0.7271 (t80) REVERT: p 7 LEU cc_start: 0.8292 (tp) cc_final: 0.7883 (tp) REVERT: p 10 GLU cc_start: 0.7837 (mp0) cc_final: 0.7400 (mp0) REVERT: p 13 LYS cc_start: 0.7669 (ptpt) cc_final: 0.7274 (ptpt) REVERT: p 43 GLU cc_start: 0.7376 (tp30) cc_final: 0.6538 (tp30) REVERT: p 102 ARG cc_start: 0.7164 (mtt-85) cc_final: 0.6952 (mtt90) REVERT: p 113 LEU cc_start: 0.8154 (pp) cc_final: 0.7929 (pp) REVERT: q 4 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7999 (mtmt) REVERT: q 16 ILE cc_start: 0.8060 (mt) cc_final: 0.7743 (mt) REVERT: q 75 TYR cc_start: 0.8257 (t80) cc_final: 0.8033 (t80) REVERT: q 80 ASN cc_start: 0.8138 (t0) cc_final: 0.7578 (t0) REVERT: q 83 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8186 (pttt) REVERT: q 93 ILE cc_start: 0.8770 (mm) cc_final: 0.8264 (mm) REVERT: q 101 ASP cc_start: 0.6288 (m-30) cc_final: 0.5735 (m-30) REVERT: r 13 ARG cc_start: 0.8672 (ttt-90) cc_final: 0.7822 (tpt-90) REVERT: s 18 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6709 (mtt180) REVERT: s 68 ASP cc_start: 0.8841 (t0) cc_final: 0.8465 (t70) REVERT: s 109 ASP cc_start: 0.7697 (p0) cc_final: 0.7093 (p0) REVERT: t 1 MET cc_start: 0.2224 (mtt) cc_final: 0.1987 (mtt) REVERT: t 11 LEU cc_start: 0.8071 (mp) cc_final: 0.7825 (mt) REVERT: t 37 ASP cc_start: 0.7102 (p0) cc_final: 0.6855 (p0) REVERT: u 39 ASN cc_start: 0.8479 (m-40) cc_final: 0.8016 (m110) REVERT: u 65 GLN cc_start: 0.8712 (mp10) cc_final: 0.8014 (mp10) REVERT: u 68 ASN cc_start: 0.7650 (m110) cc_final: 0.6116 (m110) REVERT: v 44 HIS cc_start: 0.7823 (t-90) cc_final: 0.7573 (t70) REVERT: v 50 MET cc_start: 0.8974 (mtp) cc_final: 0.8761 (mtp) REVERT: v 92 VAL cc_start: 0.6770 (p) cc_final: 0.6381 (m) REVERT: w 21 ARG cc_start: 0.8486 (mmt-90) cc_final: 0.7956 (mmm-85) REVERT: w 37 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8307 (tpp-160) REVERT: w 60 ASP cc_start: 0.8835 (t0) cc_final: 0.8461 (t0) REVERT: x 31 ASN cc_start: 0.8303 (t0) cc_final: 0.7904 (t0) REVERT: x 63 ILE cc_start: 0.7322 (tp) cc_final: 0.7070 (tp) REVERT: y 13 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8647 (tp30) REVERT: y 26 PHE cc_start: 0.8472 (t80) cc_final: 0.8165 (t80) REVERT: z 10 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7743 (mpt-90) REVERT: C 44 GLN cc_start: 0.6754 (mm110) cc_final: 0.6150 (mm110) REVERT: E 14 LYS cc_start: 0.8879 (tppt) cc_final: 0.8671 (tppt) REVERT: E 61 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7957 (pp) REVERT: F 1 MET cc_start: 0.7777 (ptp) cc_final: 0.7288 (ptm) REVERT: F 34 LYS cc_start: 0.8154 (mttt) cc_final: 0.7833 (mtmt) REVERT: F 35 GLN cc_start: 0.7120 (pt0) cc_final: 0.6530 (pm20) REVERT: G 8 MET cc_start: 0.7836 (mpp) cc_final: 0.7499 (mpp) REVERT: G 26 MET cc_start: 0.6375 (mmm) cc_final: 0.5161 (mmm) REVERT: G 34 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8332 (tpp80) REVERT: G 57 ASN cc_start: 0.8864 (t0) cc_final: 0.8511 (m-40) REVERT: G 62 ARG cc_start: 0.7360 (ttp80) cc_final: 0.7118 (ttp-110) REVERT: G 68 PHE cc_start: 0.7121 (m-80) cc_final: 0.6694 (m-80) REVERT: G 89 PHE cc_start: 0.6530 (m-80) cc_final: 0.5918 (m-80) REVERT: G 107 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.6965 (ptp90) REVERT: G 112 ARG cc_start: 0.7526 (ptm160) cc_final: 0.7213 (ptm160) REVERT: G 151 LYS cc_start: 0.8757 (tptm) cc_final: 0.8497 (mmmt) REVERT: G 212 TYR cc_start: 0.8671 (m-10) cc_final: 0.8231 (m-80) REVERT: H 33 ASP cc_start: 0.8331 (t0) cc_final: 0.7547 (t0) REVERT: H 69 THR cc_start: 0.7096 (p) cc_final: 0.6630 (t) REVERT: I 13 ARG cc_start: 0.5299 (tpp-160) cc_final: 0.4891 (tpt90) REVERT: I 77 GLU cc_start: 0.8441 (pt0) cc_final: 0.8115 (pt0) REVERT: I 80 ARG cc_start: 0.8866 (ppt170) cc_final: 0.8128 (ptm-80) REVERT: J 47 PHE cc_start: 0.8771 (p90) cc_final: 0.8328 (p90) REVERT: J 60 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7412 (tm-30) REVERT: J 70 MET cc_start: 0.7170 (mtp) cc_final: 0.6922 (tpp) REVERT: J 81 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7828 (mm110) REVERT: J 88 HIS cc_start: 0.8987 (t-90) cc_final: 0.8760 (t70) REVERT: J 134 ASN cc_start: 0.6132 (t160) cc_final: 0.5620 (t0) REVERT: J 146 MET cc_start: 0.7883 (mmm) cc_final: 0.7500 (mmm) REVERT: J 151 MET cc_start: 0.7905 (mmp) cc_final: 0.7671 (mmp) REVERT: K 14 GLN cc_start: 0.8737 (mp10) cc_final: 0.8407 (mm-40) REVERT: K 21 MET cc_start: 0.8646 (mtp) cc_final: 0.8371 (mtt) REVERT: K 40 GLU cc_start: 0.7548 (tt0) cc_final: 0.7211 (tp30) REVERT: K 72 ASP cc_start: 0.9107 (m-30) cc_final: 0.8780 (p0) REVERT: K 90 MET cc_start: 0.7784 (mmp) cc_final: 0.7112 (mmm) REVERT: L 46 LEU cc_start: 0.7414 (mt) cc_final: 0.6979 (mt) REVERT: L 47 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8671 (tm-30) REVERT: L 48 THR cc_start: 0.8904 (p) cc_final: 0.8640 (p) REVERT: L 69 ARG cc_start: 0.6748 (ttm170) cc_final: 0.6437 (ttp80) REVERT: L 108 ARG cc_start: 0.6033 (mmt90) cc_final: 0.5766 (tpt170) REVERT: L 121 ASN cc_start: 0.8837 (m-40) cc_final: 0.8549 (m110) REVERT: M 2 MET cc_start: 0.6923 (tpt) cc_final: 0.6145 (tpt) REVERT: M 9 MET cc_start: 0.6795 (ttp) cc_final: 0.5742 (tmm) REVERT: M 17 GLN cc_start: 0.9045 (mm110) cc_final: 0.8576 (mm110) REVERT: M 26 MET cc_start: 0.7471 (ptp) cc_final: 0.6690 (ptt) REVERT: M 57 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7164 (pm20) REVERT: M 72 GLU cc_start: 0.7799 (mp0) cc_final: 0.7489 (mp0) REVERT: M 95 MET cc_start: 0.7166 (ttm) cc_final: 0.6640 (ttm) REVERT: M 98 LEU cc_start: 0.8219 (pp) cc_final: 0.6889 (pp) REVERT: M 110 MET cc_start: 0.7176 (ptt) cc_final: 0.6178 (ptt) REVERT: M 111 THR cc_start: 0.7909 (p) cc_final: 0.7574 (p) REVERT: N 21 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8971 (mtmm) REVERT: N 24 ASN cc_start: 0.8969 (t0) cc_final: 0.8438 (t0) REVERT: N 67 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7504 (tptp) REVERT: N 79 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.7763 (ttt-90) REVERT: N 114 LYS cc_start: 0.7017 (mppt) cc_final: 0.6447 (mtpt) REVERT: O 7 ARG cc_start: 0.6762 (tpp80) cc_final: 0.6454 (mmt180) REVERT: O 72 ARG cc_start: 0.7228 (mmt-90) cc_final: 0.6414 (mmt180) REVERT: P 26 PHE cc_start: 0.8435 (m-80) cc_final: 0.8148 (m-80) REVERT: P 52 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.5503 (ptm160) REVERT: P 109 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7361 (mm) REVERT: P 118 ASN cc_start: 0.7530 (t0) cc_final: 0.6456 (p0) REVERT: Q 27 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7713 (Cg_endo) REVERT: Q 29 LYS cc_start: 0.6740 (tptt) cc_final: 0.6390 (mmmt) REVERT: Q 76 HIS cc_start: 0.8700 (m-70) cc_final: 0.8439 (m90) REVERT: R 2 ARG cc_start: 0.5303 (tpt170) cc_final: 0.5075 (tpt-90) REVERT: R 21 ILE cc_start: 0.8446 (mp) cc_final: 0.8123 (mp) REVERT: R 70 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8898 (mtt180) REVERT: R 72 ILE cc_start: 0.9314 (tp) cc_final: 0.9071 (tp) REVERT: R 112 ARG cc_start: 0.6620 (ttm170) cc_final: 0.5915 (ptt-90) REVERT: S 61 ASN cc_start: 0.8378 (t0) cc_final: 0.7996 (t0) REVERT: S 64 ARG cc_start: 0.6705 (tpp80) cc_final: 0.6355 (ttm110) REVERT: T 46 LYS cc_start: 0.7465 (mtmm) cc_final: 0.6977 (mmmt) REVERT: T 48 ASP cc_start: 0.7553 (t0) cc_final: 0.7257 (m-30) REVERT: T 65 LEU cc_start: 0.8539 (mm) cc_final: 0.8298 (mm) REVERT: T 82 GLU cc_start: 0.8683 (pp20) cc_final: 0.8443 (pp20) REVERT: U 26 ASN cc_start: 0.6067 (m-40) cc_final: 0.5540 (m-40) REVERT: U 32 PHE cc_start: 0.8477 (p90) cc_final: 0.8210 (p90) REVERT: U 79 ASN cc_start: 0.8180 (p0) cc_final: 0.7888 (p0) REVERT: V 24 ILE cc_start: 0.8474 (tp) cc_final: 0.8268 (tp) REVERT: V 62 GLU cc_start: 0.7378 (tp30) cc_final: 0.7149 (tp30) REVERT: V 73 THR cc_start: 0.8275 (m) cc_final: 0.7745 (m) REVERT: V 79 GLU cc_start: 0.8290 (mp0) cc_final: 0.7309 (tt0) REVERT: W 29 LYS cc_start: 0.8731 (pptt) cc_final: 0.8425 (pptt) REVERT: W 53 GLN cc_start: 0.9085 (tt0) cc_final: 0.8216 (tm-30) REVERT: W 63 TYR cc_start: 0.8376 (t80) cc_final: 0.8080 (t80) REVERT: X 63 ASP cc_start: 0.9297 (m-30) cc_final: 0.9097 (m-30) REVERT: X 65 MET cc_start: 0.8067 (ptt) cc_final: 0.7652 (ptt) REVERT: X 80 ARG cc_start: 0.4955 (mtt180) cc_final: 0.4699 (mtt180) REVERT: Y 9 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8278 (tpp80) REVERT: Y 15 LYS cc_start: 0.9132 (tppt) cc_final: 0.8863 (tmmt) REVERT: Y 26 MET cc_start: 0.8565 (ppp) cc_final: 0.8350 (ppp) REVERT: Y 30 PHE cc_start: 0.9147 (m-80) cc_final: 0.8565 (m-80) REVERT: Y 34 VAL cc_start: 0.8916 (t) cc_final: 0.8492 (t) REVERT: Y 42 ASP cc_start: 0.9024 (t0) cc_final: 0.8770 (t0) REVERT: Y 50 PHE cc_start: 0.9103 (t80) cc_final: 0.8788 (t80) REVERT: Y 63 LYS cc_start: 0.8156 (mmpt) cc_final: 0.7028 (mmpt) REVERT: Z 18 PHE cc_start: 0.7987 (t80) cc_final: 0.7508 (t80) REVERT: a 7 ARG cc_start: 0.6532 (tpt90) cc_final: 0.6084 (mtt180) REVERT: a 167 LYS cc_start: 0.8849 (mttt) cc_final: 0.8487 (mmtt) outliers start: 13 outliers final: 6 residues processed: 1590 average time/residue: 1.4399 time to fit residues: 3832.5741 Evaluate side-chains 1311 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1303 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 10.0000 chunk 856 optimal weight: 20.0000 chunk 953 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 771 optimal weight: 10.0000 overall best weight: 8.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN c 32 ASN c 140 HIS ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 HIS j 80 HIS ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 22 GLN n 11 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 11 GLN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN x 5 GLN y 20 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 GLN z 8 GLN F 35 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN I 151 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN L 67 ASN M 66 GLN M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN O 56 HIS ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 163139 Z= 0.398 Angle : 0.861 16.442 244082 Z= 0.437 Chirality : 0.045 0.295 31220 Planarity : 0.007 0.077 13080 Dihedral : 23.552 178.303 81722 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.82 % Favored : 86.04 % Rotamer: Outliers : 0.12 % Allowed : 8.41 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.10), residues: 5919 helix: -1.86 (0.11), residues: 1773 sheet: -2.43 (0.16), residues: 828 loop : -2.86 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP b 212 HIS 0.017 0.002 HIS b 52 PHE 0.048 0.003 PHE v 2 TYR 0.032 0.003 TYR j 44 ARG 0.022 0.001 ARG b 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1512 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1506 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 47 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7416 (mtt-85) REVERT: b 99 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7696 (mm-30) REVERT: b 200 MET cc_start: 0.8175 (ptt) cc_final: 0.7215 (tmm) REVERT: b 212 TRP cc_start: 0.8327 (p90) cc_final: 0.8066 (p90) REVERT: b 259 ASN cc_start: 0.8313 (t0) cc_final: 0.7991 (t0) REVERT: c 8 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8182 (ptmt) REVERT: c 82 PHE cc_start: 0.7716 (m-80) cc_final: 0.7280 (m-80) REVERT: c 141 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8579 (mtp85) REVERT: c 156 PHE cc_start: 0.7665 (m-80) cc_final: 0.7313 (m-80) REVERT: c 183 GLU cc_start: 0.9323 (mp0) cc_final: 0.8976 (mp0) REVERT: d 25 GLU cc_start: 0.7451 (tt0) cc_final: 0.7117 (tt0) REVERT: d 51 GLU cc_start: 0.8270 (tt0) cc_final: 0.7958 (tt0) REVERT: d 136 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7822 (tp-100) REVERT: d 140 ASP cc_start: 0.7679 (m-30) cc_final: 0.7128 (m-30) REVERT: d 156 ASN cc_start: 0.8941 (m-40) cc_final: 0.8346 (t0) REVERT: d 166 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7631 (mmmt) REVERT: d 183 PHE cc_start: 0.6103 (m-80) cc_final: 0.5016 (m-80) REVERT: d 188 MET cc_start: 0.5743 (ptp) cc_final: 0.5083 (ptm) REVERT: d 194 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9197 (mmmt) REVERT: e 28 PRO cc_start: 0.8449 (Cg_exo) cc_final: 0.8240 (Cg_endo) REVERT: e 90 LEU cc_start: 0.9123 (tp) cc_final: 0.8691 (tp) REVERT: e 174 PHE cc_start: 0.6093 (m-10) cc_final: 0.5759 (m-80) REVERT: f 31 GLU cc_start: 0.7333 (tt0) cc_final: 0.7041 (tm-30) REVERT: f 41 GLU cc_start: 0.8884 (tt0) cc_final: 0.8622 (tm-30) REVERT: f 103 ASN cc_start: 0.8777 (t0) cc_final: 0.8540 (t0) REVERT: g 17 ASP cc_start: 0.8337 (m-30) cc_final: 0.8029 (m-30) REVERT: g 43 ASN cc_start: 0.8298 (m110) cc_final: 0.7664 (m-40) REVERT: h 1 MET cc_start: 0.4303 (ttp) cc_final: 0.1936 (tmm) REVERT: i 116 MET cc_start: -0.1101 (ttt) cc_final: -0.1311 (ttt) REVERT: j 31 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7621 (mm-30) REVERT: j 41 LYS cc_start: 0.8880 (mttt) cc_final: 0.8495 (mttt) REVERT: j 71 ASP cc_start: 0.8436 (m-30) cc_final: 0.7667 (m-30) REVERT: j 106 LYS cc_start: 0.8376 (tptt) cc_final: 0.8045 (tptt) REVERT: j 108 MET cc_start: 0.8148 (mtt) cc_final: 0.7411 (mtt) REVERT: j 118 MET cc_start: 0.8874 (ptp) cc_final: 0.8458 (ptp) REVERT: j 119 PHE cc_start: 0.8166 (t80) cc_final: 0.7945 (t80) REVERT: k 2 ILE cc_start: 0.8448 (mm) cc_final: 0.8065 (mm) REVERT: k 64 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7509 (mtm180) REVERT: k 98 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7863 (ttp-110) REVERT: l 57 LEU cc_start: 0.8940 (tp) cc_final: 0.8706 (tp) REVERT: m 33 LEU cc_start: 0.6510 (tp) cc_final: 0.5978 (tt) REVERT: m 81 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6320 (mtt180) REVERT: n 17 ARG cc_start: 0.8736 (ttp-110) cc_final: 0.8366 (ttp-110) REVERT: n 46 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8399 (ttm110) REVERT: n 73 ASN cc_start: 0.8658 (m-40) cc_final: 0.8082 (m110) REVERT: n 99 LYS cc_start: 0.7766 (mttt) cc_final: 0.7522 (mmtp) REVERT: o 4 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8627 (mmmt) REVERT: o 17 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8152 (mmtt) REVERT: o 18 LEU cc_start: 0.8627 (pt) cc_final: 0.8403 (pt) REVERT: o 19 GLN cc_start: 0.9196 (pp30) cc_final: 0.8500 (pp30) REVERT: o 38 GLN cc_start: 0.7671 (pt0) cc_final: 0.6733 (pm20) REVERT: o 92 PHE cc_start: 0.7579 (t80) cc_final: 0.7330 (t80) REVERT: o 93 ASP cc_start: 0.8395 (t0) cc_final: 0.8163 (t0) REVERT: o 98 GLN cc_start: 0.7097 (tp-100) cc_final: 0.6837 (tp40) REVERT: o 117 PHE cc_start: 0.6408 (p90) cc_final: 0.6195 (p90) REVERT: p 43 GLU cc_start: 0.7468 (tp30) cc_final: 0.6901 (tp30) REVERT: p 113 LEU cc_start: 0.8271 (pp) cc_final: 0.8045 (pp) REVERT: q 4 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8156 (mtmt) REVERT: q 16 ILE cc_start: 0.8243 (mt) cc_final: 0.7887 (mt) REVERT: q 93 ILE cc_start: 0.8919 (mm) cc_final: 0.8493 (mm) REVERT: r 13 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.7707 (tpt-90) REVERT: r 34 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8620 (tm-30) REVERT: r 35 PHE cc_start: 0.8442 (m-80) cc_final: 0.8007 (m-80) REVERT: s 68 ASP cc_start: 0.9018 (t0) cc_final: 0.8201 (t70) REVERT: s 109 ASP cc_start: 0.7606 (p0) cc_final: 0.5593 (t0) REVERT: t 1 MET cc_start: 0.1999 (mtt) cc_final: 0.1707 (mtt) REVERT: u 39 ASN cc_start: 0.8241 (m-40) cc_final: 0.7585 (m110) REVERT: u 65 GLN cc_start: 0.8697 (mp10) cc_final: 0.8200 (mp10) REVERT: u 68 ASN cc_start: 0.7694 (m110) cc_final: 0.6934 (m110) REVERT: u 98 ASN cc_start: 0.8668 (t0) cc_final: 0.8446 (t0) REVERT: u 100 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8447 (mm-30) REVERT: v 44 HIS cc_start: 0.7718 (t-90) cc_final: 0.7438 (t70) REVERT: v 46 LYS cc_start: 0.9640 (mtpt) cc_final: 0.9255 (mtmm) REVERT: v 50 MET cc_start: 0.8967 (mtp) cc_final: 0.8624 (mtp) REVERT: v 76 ASP cc_start: 0.7910 (m-30) cc_final: 0.7659 (m-30) REVERT: w 21 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7852 (mmm-85) REVERT: w 51 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7836 (ptm-80) REVERT: w 60 ASP cc_start: 0.8805 (t0) cc_final: 0.8454 (t0) REVERT: x 31 ASN cc_start: 0.8077 (t0) cc_final: 0.7565 (t0) REVERT: y 26 PHE cc_start: 0.8645 (t80) cc_final: 0.8393 (t80) REVERT: y 45 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6373 (pp30) REVERT: y 49 ASP cc_start: 0.8012 (m-30) cc_final: 0.7543 (m-30) REVERT: z 55 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8204 (tptt) REVERT: E 29 ARG cc_start: 0.8471 (mmt180) cc_final: 0.8221 (mmt-90) REVERT: E 61 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8285 (pp) REVERT: F 1 MET cc_start: 0.7686 (ptp) cc_final: 0.7005 (ptp) REVERT: F 34 LYS cc_start: 0.8081 (mttt) cc_final: 0.7832 (mttt) REVERT: F 35 GLN cc_start: 0.7189 (pt0) cc_final: 0.6772 (pm20) REVERT: G 8 MET cc_start: 0.8144 (mpp) cc_final: 0.7777 (mpp) REVERT: G 21 TYR cc_start: 0.7022 (m-10) cc_final: 0.6653 (m-10) REVERT: G 22 TRP cc_start: 0.5965 (p-90) cc_final: 0.5419 (p-90) REVERT: G 26 MET cc_start: 0.6799 (mmm) cc_final: 0.5402 (mmm) REVERT: G 34 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8317 (tpp80) REVERT: G 57 ASN cc_start: 0.8902 (t0) cc_final: 0.8505 (m-40) REVERT: G 68 PHE cc_start: 0.7139 (m-80) cc_final: 0.6807 (m-80) REVERT: G 89 PHE cc_start: 0.6692 (m-80) cc_final: 0.6067 (m-80) REVERT: G 117 GLU cc_start: 0.5278 (mp0) cc_final: 0.4697 (mm-30) REVERT: G 121 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8922 (mm-40) REVERT: G 162 VAL cc_start: 0.6940 (t) cc_final: 0.6702 (t) REVERT: G 212 TYR cc_start: 0.8741 (m-10) cc_final: 0.8237 (m-80) REVERT: H 165 GLU cc_start: 0.5687 (tm-30) cc_final: 0.5042 (tm-30) REVERT: I 13 ARG cc_start: 0.5130 (tpp-160) cc_final: 0.4484 (tpt170) REVERT: I 50 TYR cc_start: 0.7200 (t80) cc_final: 0.6989 (t80) REVERT: I 76 LYS cc_start: 0.5902 (mptt) cc_final: 0.5286 (mptt) REVERT: I 80 ARG cc_start: 0.8935 (ppt170) cc_final: 0.8228 (ptm-80) REVERT: J 47 PHE cc_start: 0.8764 (p90) cc_final: 0.8422 (p90) REVERT: J 70 MET cc_start: 0.7951 (mtp) cc_final: 0.7487 (mtt) REVERT: J 88 HIS cc_start: 0.8973 (t-90) cc_final: 0.8658 (t-90) REVERT: J 96 GLN cc_start: 0.7920 (tp40) cc_final: 0.7437 (mm110) REVERT: J 134 ASN cc_start: 0.6370 (t0) cc_final: 0.5737 (t0) REVERT: K 21 MET cc_start: 0.8714 (mtp) cc_final: 0.8416 (mtt) REVERT: K 40 GLU cc_start: 0.7551 (tt0) cc_final: 0.7109 (tp30) REVERT: K 72 ASP cc_start: 0.9188 (m-30) cc_final: 0.8830 (p0) REVERT: L 47 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8609 (tm-30) REVERT: L 48 THR cc_start: 0.8718 (p) cc_final: 0.8295 (p) REVERT: L 69 ARG cc_start: 0.6837 (ttm170) cc_final: 0.6592 (ttp80) REVERT: L 121 ASN cc_start: 0.8811 (m-40) cc_final: 0.8434 (m-40) REVERT: M 8 ASP cc_start: 0.8453 (m-30) cc_final: 0.7553 (m-30) REVERT: M 9 MET cc_start: 0.6304 (ttp) cc_final: 0.5061 (tmm) REVERT: M 26 MET cc_start: 0.7837 (ptp) cc_final: 0.7158 (ptt) REVERT: M 57 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7268 (pm20) REVERT: M 87 ARG cc_start: 0.7225 (tpp80) cc_final: 0.6303 (tpp-160) REVERT: N 5 TYR cc_start: 0.8716 (m-10) cc_final: 0.8306 (m-80) REVERT: N 21 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9127 (mtmm) REVERT: N 24 ASN cc_start: 0.9144 (t0) cc_final: 0.8703 (t0) REVERT: N 67 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7386 (tptp) REVERT: N 74 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8653 (mm110) REVERT: N 98 ARG cc_start: 0.8574 (tmt-80) cc_final: 0.8314 (tmt-80) REVERT: N 114 LYS cc_start: 0.7218 (mppt) cc_final: 0.6940 (mtpt) REVERT: O 66 GLU cc_start: 0.8073 (pp20) cc_final: 0.7586 (pp20) REVERT: O 72 ARG cc_start: 0.7125 (mmt-90) cc_final: 0.6151 (mmm-85) REVERT: O 88 MET cc_start: 0.4640 (mmt) cc_final: 0.3725 (ppp) REVERT: P 124 LYS cc_start: 0.6525 (pttm) cc_final: 0.6140 (tmtt) REVERT: Q 13 ARG cc_start: 0.8234 (tmt-80) cc_final: 0.8016 (tmt-80) REVERT: R 21 ILE cc_start: 0.8628 (mp) cc_final: 0.8371 (mp) REVERT: R 69 ARG cc_start: 0.8167 (tmm160) cc_final: 0.7811 (ttp80) REVERT: R 70 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8416 (mtt180) REVERT: R 112 ARG cc_start: 0.6222 (ttm170) cc_final: 0.5701 (ptt-90) REVERT: S 61 ASN cc_start: 0.8549 (t0) cc_final: 0.8219 (t0) REVERT: T 34 GLN cc_start: 0.7935 (mp10) cc_final: 0.7678 (mp10) REVERT: T 46 LYS cc_start: 0.7245 (mtmm) cc_final: 0.6833 (mmmm) REVERT: U 26 ASN cc_start: 0.6815 (m-40) cc_final: 0.6493 (m110) REVERT: U 77 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8766 (mm-30) REVERT: U 79 ASN cc_start: 0.8246 (p0) cc_final: 0.7935 (p0) REVERT: V 79 GLU cc_start: 0.8292 (mp0) cc_final: 0.7188 (tt0) REVERT: W 42 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7609 (ttt180) REVERT: W 63 TYR cc_start: 0.8507 (t80) cc_final: 0.7812 (t80) REVERT: X 65 MET cc_start: 0.7638 (ptt) cc_final: 0.7309 (ptt) REVERT: X 80 ARG cc_start: 0.5388 (mtt180) cc_final: 0.5119 (mtt180) REVERT: Y 26 MET cc_start: 0.8579 (ppp) cc_final: 0.8266 (ppp) REVERT: Y 30 PHE cc_start: 0.9059 (m-80) cc_final: 0.8304 (m-80) REVERT: Y 42 ASP cc_start: 0.8986 (t0) cc_final: 0.8616 (t0) REVERT: Y 50 PHE cc_start: 0.9202 (t80) cc_final: 0.8962 (t80) REVERT: Y 56 ILE cc_start: 0.9349 (mt) cc_final: 0.9103 (mt) REVERT: Y 78 LEU cc_start: 0.8928 (mm) cc_final: 0.8710 (mm) REVERT: Z 18 PHE cc_start: 0.7390 (t80) cc_final: 0.7048 (t80) REVERT: Z 28 LEU cc_start: 0.7392 (tt) cc_final: 0.6626 (tt) REVERT: a 7 ARG cc_start: 0.6694 (tpt90) cc_final: 0.6139 (mtt180) REVERT: a 167 LYS cc_start: 0.8910 (mttt) cc_final: 0.8567 (mmtt) outliers start: 6 outliers final: 1 residues processed: 1510 average time/residue: 1.4062 time to fit residues: 3560.0032 Evaluate side-chains 1267 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1264 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 50.0000 chunk 722 optimal weight: 10.0000 chunk 499 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 458 optimal weight: 50.0000 chunk 645 optimal weight: 20.0000 chunk 965 optimal weight: 9.9990 chunk 1021 optimal weight: 10.0000 chunk 504 optimal weight: 0.1980 chunk 914 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 199 HIS c 140 HIS ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN i 30 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 13 HIS ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 ASN n 62 ASN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS s 31 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 78 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS E 30 HIS F 35 GLN H 138 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 163139 Z= 0.296 Angle : 0.735 15.971 244082 Z= 0.376 Chirality : 0.041 0.329 31220 Planarity : 0.006 0.087 13080 Dihedral : 23.616 179.025 81722 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.49 % Favored : 88.39 % Rotamer: Outliers : 0.14 % Allowed : 4.52 % Favored : 95.33 % 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: -3.42 (0.10), residues: 5919 helix: -1.56 (0.11), residues: 1792 sheet: -2.40 (0.16), residues: 882 loop : -2.71 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 212 HIS 0.017 0.002 HIS c 67 PHE 0.037 0.003 PHE t 51 TYR 0.023 0.002 TYR I 75 ARG 0.013 0.001 ARG b 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1497 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 32 LEU cc_start: 0.8957 (mt) cc_final: 0.8566 (mt) REVERT: b 99 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7622 (mm-30) REVERT: b 131 MET cc_start: 0.8861 (mpp) cc_final: 0.8564 (mpp) REVERT: b 200 MET cc_start: 0.8324 (ptt) cc_final: 0.8030 (tmm) REVERT: b 267 VAL cc_start: 0.9140 (t) cc_final: 0.8209 (t) REVERT: c 134 HIS cc_start: 0.8063 (m90) cc_final: 0.7709 (m90) REVERT: c 156 PHE cc_start: 0.7728 (m-80) cc_final: 0.7406 (m-80) REVERT: d 25 GLU cc_start: 0.7153 (tt0) cc_final: 0.6756 (tt0) REVERT: d 51 GLU cc_start: 0.8015 (tt0) cc_final: 0.7645 (tt0) REVERT: d 74 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8288 (ttmt) REVERT: d 106 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7261 (mttm) REVERT: d 183 PHE cc_start: 0.6103 (m-80) cc_final: 0.5104 (m-80) REVERT: d 188 MET cc_start: 0.5464 (ptp) cc_final: 0.4936 (ptm) REVERT: e 82 TYR cc_start: 0.7618 (t80) cc_final: 0.6911 (t80) REVERT: e 90 LEU cc_start: 0.9087 (tp) cc_final: 0.8851 (tp) REVERT: f 41 GLU cc_start: 0.8920 (tt0) cc_final: 0.8345 (tm-30) REVERT: f 43 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8447 (ptpp) REVERT: f 61 TRP cc_start: 0.7090 (m100) cc_final: 0.6669 (m-90) REVERT: f 74 MET cc_start: 0.6768 (tmm) cc_final: 0.6305 (tmm) REVERT: f 127 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7544 (mm-40) REVERT: g 7 ASP cc_start: 0.6615 (p0) cc_final: 0.6307 (p0) REVERT: h 1 MET cc_start: 0.4390 (ttp) cc_final: 0.2001 (tmm) REVERT: i 135 MET cc_start: 0.5752 (ptp) cc_final: 0.5211 (mmt) REVERT: j 14 ASP cc_start: 0.7703 (m-30) cc_final: 0.7396 (m-30) REVERT: j 31 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7332 (mm-30) REVERT: j 41 LYS cc_start: 0.8865 (mttt) cc_final: 0.8459 (mttt) REVERT: j 71 ASP cc_start: 0.8411 (m-30) cc_final: 0.7813 (m-30) REVERT: j 106 LYS cc_start: 0.8109 (tptt) cc_final: 0.7776 (tptt) REVERT: k 2 ILE cc_start: 0.8321 (mm) cc_final: 0.7707 (mm) REVERT: k 29 HIS cc_start: 0.8467 (t70) cc_final: 0.8194 (t70) REVERT: k 71 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7646 (ttt180) REVERT: k 98 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7751 (ttp-110) REVERT: k 116 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8454 (pt) REVERT: m 33 LEU cc_start: 0.6502 (tp) cc_final: 0.6223 (tt) REVERT: m 53 MET cc_start: 0.6708 (ttm) cc_final: 0.6341 (tmm) REVERT: m 81 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6167 (mtt180) REVERT: m 111 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7920 (tp30) REVERT: n 17 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8313 (ttp-110) REVERT: n 35 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8910 (ttpp) REVERT: n 73 ASN cc_start: 0.8596 (m-40) cc_final: 0.8078 (m-40) REVERT: o 4 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8394 (mmmt) REVERT: o 17 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8102 (mmtt) REVERT: o 18 LEU cc_start: 0.8691 (pt) cc_final: 0.8467 (pt) REVERT: o 38 GLN cc_start: 0.7644 (pt0) cc_final: 0.6513 (pm20) REVERT: o 40 ILE cc_start: 0.6953 (mt) cc_final: 0.5718 (mt) REVERT: o 92 PHE cc_start: 0.7431 (t80) cc_final: 0.7214 (t80) REVERT: p 7 LEU cc_start: 0.8560 (tp) cc_final: 0.8281 (tp) REVERT: p 10 GLU cc_start: 0.7735 (mp0) cc_final: 0.7443 (mp0) REVERT: p 43 GLU cc_start: 0.7373 (tp30) cc_final: 0.6591 (tp30) REVERT: p 109 ILE cc_start: 0.8460 (pt) cc_final: 0.8145 (mm) REVERT: q 4 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8048 (mtmt) REVERT: q 16 ILE cc_start: 0.8099 (mt) cc_final: 0.7772 (mt) REVERT: q 83 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8110 (ttpt) REVERT: q 93 ILE cc_start: 0.8828 (mm) cc_final: 0.8456 (mm) REVERT: r 11 GLN cc_start: 0.8479 (mp10) cc_final: 0.8242 (mp10) REVERT: r 13 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8211 (ttt-90) REVERT: r 22 LEU cc_start: 0.6209 (pp) cc_final: 0.5708 (pp) REVERT: r 35 PHE cc_start: 0.8534 (m-80) cc_final: 0.8228 (m-10) REVERT: r 85 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7412 (mtmt) REVERT: s 31 GLN cc_start: 0.7919 (tt0) cc_final: 0.7624 (tt0) REVERT: s 68 ASP cc_start: 0.9057 (t0) cc_final: 0.8311 (t0) REVERT: s 78 GLU cc_start: 0.8492 (tp30) cc_final: 0.8075 (tp30) REVERT: s 109 ASP cc_start: 0.7595 (p0) cc_final: 0.5758 (t0) REVERT: t 1 MET cc_start: 0.1851 (mtt) cc_final: 0.1637 (mtt) REVERT: t 11 LEU cc_start: 0.7664 (mt) cc_final: 0.7199 (mt) REVERT: u 39 ASN cc_start: 0.8145 (m-40) cc_final: 0.7488 (m110) REVERT: u 65 GLN cc_start: 0.8264 (mp10) cc_final: 0.8002 (mp10) REVERT: u 68 ASN cc_start: 0.7614 (m110) cc_final: 0.6456 (m110) REVERT: u 78 LYS cc_start: 0.8829 (pttm) cc_final: 0.8519 (pttm) REVERT: v 30 ILE cc_start: 0.8981 (tt) cc_final: 0.8778 (tt) REVERT: v 46 LYS cc_start: 0.9623 (mtpt) cc_final: 0.9162 (mtmm) REVERT: v 50 MET cc_start: 0.8869 (mtp) cc_final: 0.8214 (mtt) REVERT: v 76 ASP cc_start: 0.7659 (m-30) cc_final: 0.7368 (m-30) REVERT: w 21 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8071 (mmm-85) REVERT: w 60 ASP cc_start: 0.8747 (t0) cc_final: 0.8463 (t0) REVERT: x 31 ASN cc_start: 0.8123 (t0) cc_final: 0.7614 (t0) REVERT: x 63 ILE cc_start: 0.7178 (tp) cc_final: 0.6973 (tp) REVERT: y 26 PHE cc_start: 0.8468 (t80) cc_final: 0.8125 (t80) REVERT: B 47 TYR cc_start: 0.6958 (m-80) cc_final: 0.6677 (m-80) REVERT: F 1 MET cc_start: 0.7670 (ptp) cc_final: 0.6714 (ptp) REVERT: F 24 ARG cc_start: 0.7270 (mtt-85) cc_final: 0.6942 (mmt90) REVERT: F 34 LYS cc_start: 0.8038 (mttt) cc_final: 0.7833 (mttt) REVERT: F 35 GLN cc_start: 0.7108 (pt0) cc_final: 0.6762 (pm20) REVERT: G 8 MET cc_start: 0.8226 (mpp) cc_final: 0.7856 (mpp) REVERT: G 21 TYR cc_start: 0.6911 (m-10) cc_final: 0.6568 (m-10) REVERT: G 22 TRP cc_start: 0.6427 (p-90) cc_final: 0.5937 (p-90) REVERT: G 26 MET cc_start: 0.6587 (mmm) cc_final: 0.5281 (mmm) REVERT: G 57 ASN cc_start: 0.8823 (t0) cc_final: 0.8536 (m-40) REVERT: G 89 PHE cc_start: 0.6290 (m-80) cc_final: 0.6062 (m-80) REVERT: G 121 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8922 (mm-40) REVERT: G 132 GLU cc_start: 0.5564 (mm-30) cc_final: 0.5271 (tp30) REVERT: G 172 ILE cc_start: 0.8289 (mm) cc_final: 0.8067 (mm) REVERT: G 212 TYR cc_start: 0.8762 (m-10) cc_final: 0.8316 (m-80) REVERT: H 69 THR cc_start: 0.7167 (p) cc_final: 0.6787 (t) REVERT: H 141 MET cc_start: 0.8215 (mmt) cc_final: 0.7741 (mmt) REVERT: H 165 GLU cc_start: 0.5140 (tm-30) cc_final: 0.4639 (tm-30) REVERT: I 13 ARG cc_start: 0.5170 (tpp-160) cc_final: 0.4594 (tpt170) REVERT: I 50 TYR cc_start: 0.7276 (t80) cc_final: 0.6959 (t80) REVERT: I 76 LYS cc_start: 0.5687 (mptt) cc_final: 0.5240 (mptt) REVERT: J 47 PHE cc_start: 0.8743 (p90) cc_final: 0.8427 (p90) REVERT: J 64 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8464 (mt-10) REVERT: J 70 MET cc_start: 0.7517 (mtp) cc_final: 0.6947 (mtt) REVERT: J 96 GLN cc_start: 0.7900 (tp40) cc_final: 0.7355 (mm110) REVERT: J 127 TYR cc_start: 0.6263 (m-80) cc_final: 0.5891 (m-80) REVERT: J 150 GLU cc_start: 0.8860 (pm20) cc_final: 0.8598 (pm20) REVERT: J 151 MET cc_start: 0.8295 (mmt) cc_final: 0.8050 (mmp) REVERT: K 40 GLU cc_start: 0.7623 (tt0) cc_final: 0.7162 (tp30) REVERT: K 72 ASP cc_start: 0.9148 (m-30) cc_final: 0.8826 (p0) REVERT: L 47 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8576 (tm-30) REVERT: L 49 LEU cc_start: 0.9168 (pp) cc_final: 0.8888 (mm) REVERT: L 100 MET cc_start: 0.4047 (mtp) cc_final: 0.3837 (mtp) REVERT: L 121 ASN cc_start: 0.8560 (m-40) cc_final: 0.8154 (m-40) REVERT: M 2 MET cc_start: 0.6719 (tpt) cc_final: 0.6214 (tpt) REVERT: M 8 ASP cc_start: 0.8488 (m-30) cc_final: 0.7916 (m-30) REVERT: M 9 MET cc_start: 0.6606 (ttp) cc_final: 0.5618 (tmm) REVERT: M 26 MET cc_start: 0.7602 (ptp) cc_final: 0.6950 (ptt) REVERT: M 57 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7243 (pm20) REVERT: M 72 GLU cc_start: 0.7593 (mp0) cc_final: 0.7317 (mp0) REVERT: M 87 ARG cc_start: 0.7082 (tpp80) cc_final: 0.6011 (tpp-160) REVERT: M 95 MET cc_start: 0.7499 (tpp) cc_final: 0.6984 (tpp) REVERT: N 5 TYR cc_start: 0.8739 (m-10) cc_final: 0.8428 (m-80) REVERT: N 24 ASN cc_start: 0.9093 (t0) cc_final: 0.8584 (t0) REVERT: N 67 LYS cc_start: 0.8034 (ptpp) cc_final: 0.7175 (tptp) REVERT: N 114 LYS cc_start: 0.7014 (mppt) cc_final: 0.6773 (mtpt) REVERT: O 66 GLU cc_start: 0.8101 (pp20) cc_final: 0.7516 (tm-30) REVERT: O 72 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6285 (mmm160) REVERT: O 88 MET cc_start: 0.4828 (mmt) cc_final: 0.3975 (ppp) REVERT: R 2 ARG cc_start: 0.5442 (tpt170) cc_final: 0.5106 (tpt-90) REVERT: R 21 ILE cc_start: 0.8474 (mp) cc_final: 0.8005 (mp) REVERT: R 69 ARG cc_start: 0.8160 (tmm160) cc_final: 0.7848 (ttp80) REVERT: R 70 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8358 (mtt180) REVERT: R 74 MET cc_start: 0.8298 (ppp) cc_final: 0.8046 (ppp) REVERT: R 112 ARG cc_start: 0.6065 (ttm170) cc_final: 0.5598 (ptt-90) REVERT: S 61 ASN cc_start: 0.8394 (t0) cc_final: 0.8092 (t0) REVERT: T 5 GLU cc_start: 0.7699 (tp30) cc_final: 0.7433 (tp30) REVERT: T 14 PHE cc_start: 0.8571 (m-80) cc_final: 0.8237 (m-80) REVERT: T 46 LYS cc_start: 0.7356 (mtmm) cc_final: 0.6929 (mmmt) REVERT: T 79 GLN cc_start: 0.8439 (pp30) cc_final: 0.8053 (pp30) REVERT: U 26 ASN cc_start: 0.6623 (m-40) cc_final: 0.6358 (m110) REVERT: U 77 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8744 (mm-30) REVERT: U 79 ASN cc_start: 0.8269 (p0) cc_final: 0.7953 (p0) REVERT: V 24 ILE cc_start: 0.8509 (tp) cc_final: 0.8300 (tp) REVERT: V 79 GLU cc_start: 0.8075 (mp0) cc_final: 0.6992 (tt0) REVERT: W 51 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8689 (tp-100) REVERT: W 63 TYR cc_start: 0.8503 (t80) cc_final: 0.8295 (t80) REVERT: X 65 MET cc_start: 0.7639 (ptt) cc_final: 0.7321 (ptt) REVERT: X 80 ARG cc_start: 0.5030 (mtt180) cc_final: 0.4763 (mtt180) REVERT: Y 7 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8804 (pttm) REVERT: Y 15 LYS cc_start: 0.9026 (pptt) cc_final: 0.8805 (pptt) REVERT: Y 26 MET cc_start: 0.8535 (ppp) cc_final: 0.8265 (ppp) REVERT: Y 30 PHE cc_start: 0.8955 (m-80) cc_final: 0.8198 (m-80) REVERT: Y 78 LEU cc_start: 0.8914 (mm) cc_final: 0.8640 (mm) REVERT: Z 18 PHE cc_start: 0.7561 (t80) cc_final: 0.7335 (t80) REVERT: a 7 ARG cc_start: 0.6675 (tpt90) cc_final: 0.6145 (mtt180) REVERT: a 167 LYS cc_start: 0.9006 (mttt) cc_final: 0.8649 (mmtt) outliers start: 7 outliers final: 1 residues processed: 1501 average time/residue: 1.4063 time to fit residues: 3557.3871 Evaluate side-chains 1264 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1262 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 20.0000 chunk 579 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 760 optimal weight: 30.0000 chunk 421 optimal weight: 5.9990 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 521 optimal weight: 5.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 199 HIS b 259 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN r 89 HIS ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN ** v 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 5 GLN x 22 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS D 16 HIS F 35 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 11 HIS L 67 ASN M 117 GLN N 4 GLN N 36 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 HIS ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN Y 74 HIS a 168 ASN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 163139 Z= 0.330 Angle : 0.783 15.486 244082 Z= 0.397 Chirality : 0.042 0.353 31220 Planarity : 0.006 0.073 13080 Dihedral : 23.824 179.174 81722 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.57 % Favored : 86.33 % Rotamer: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % 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: -3.32 (0.10), residues: 5919 helix: -1.44 (0.11), residues: 1759 sheet: -2.30 (0.16), residues: 875 loop : -2.68 (0.10), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP b 212 HIS 0.015 0.002 HIS v 44 PHE 0.034 0.003 PHE g 46 TYR 0.031 0.003 TYR Q 65 ARG 0.034 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1467 time to evaluate : 6.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 99 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7538 (mm-30) REVERT: b 131 MET cc_start: 0.8478 (mpp) cc_final: 0.8158 (mpp) REVERT: b 155 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8407 (mtm110) REVERT: b 193 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6369 (tm-30) REVERT: b 200 MET cc_start: 0.8119 (ptt) cc_final: 0.7546 (tmm) REVERT: b 212 TRP cc_start: 0.8540 (p90) cc_final: 0.8118 (p90) REVERT: c 36 GLN cc_start: 0.8396 (mt0) cc_final: 0.7517 (mp10) REVERT: c 80 TRP cc_start: 0.7940 (m-90) cc_final: 0.7610 (m-90) REVERT: c 175 LEU cc_start: 0.8105 (mt) cc_final: 0.7887 (mt) REVERT: c 183 GLU cc_start: 0.9276 (mp0) cc_final: 0.8853 (mp0) REVERT: d 25 GLU cc_start: 0.7102 (tt0) cc_final: 0.6721 (tt0) REVERT: d 51 GLU cc_start: 0.8113 (tt0) cc_final: 0.7699 (tt0) REVERT: d 74 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8341 (ttmt) REVERT: d 99 LYS cc_start: 0.5981 (mttt) cc_final: 0.5677 (ttpp) REVERT: d 106 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7463 (mttm) REVERT: d 136 GLN cc_start: 0.7626 (pp30) cc_final: 0.7288 (pp30) REVERT: d 188 MET cc_start: 0.5491 (ptp) cc_final: 0.5014 (ptm) REVERT: d 194 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9232 (mmmt) REVERT: e 21 TYR cc_start: 0.7876 (m-10) cc_final: 0.7492 (m-10) REVERT: e 32 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8681 (tmtt) REVERT: e 82 TYR cc_start: 0.7663 (t80) cc_final: 0.7044 (t80) REVERT: e 89 THR cc_start: 0.8807 (p) cc_final: 0.8258 (p) REVERT: e 90 LEU cc_start: 0.9282 (tp) cc_final: 0.8841 (tp) REVERT: e 110 ILE cc_start: 0.9308 (mt) cc_final: 0.9078 (mm) REVERT: e 133 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6150 (mm-30) REVERT: e 136 ILE cc_start: 0.6655 (pt) cc_final: 0.6293 (mt) REVERT: f 41 GLU cc_start: 0.8884 (tt0) cc_final: 0.8482 (tp30) REVERT: f 127 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7509 (mm-40) REVERT: f 133 LYS cc_start: 0.7096 (tptt) cc_final: 0.6767 (tppt) REVERT: g 7 ASP cc_start: 0.6588 (p0) cc_final: 0.6296 (p0) REVERT: i 135 MET cc_start: 0.5754 (ptp) cc_final: 0.5547 (mmt) REVERT: j 14 ASP cc_start: 0.7455 (m-30) cc_final: 0.7169 (m-30) REVERT: j 31 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7452 (mm-30) REVERT: j 41 LYS cc_start: 0.8829 (mttt) cc_final: 0.8569 (mttt) REVERT: j 67 ASN cc_start: 0.7359 (t0) cc_final: 0.7001 (t0) REVERT: j 71 ASP cc_start: 0.8376 (m-30) cc_final: 0.7586 (m-30) REVERT: j 99 ARG cc_start: 0.8434 (mmm160) cc_final: 0.7960 (mmm160) REVERT: j 106 LYS cc_start: 0.8231 (tptt) cc_final: 0.7939 (tptt) REVERT: k 20 MET cc_start: 0.7555 (tpt) cc_final: 0.7150 (tpt) REVERT: k 29 HIS cc_start: 0.8503 (t70) cc_final: 0.8193 (t70) REVERT: k 71 ARG cc_start: 0.8052 (tpt-90) cc_final: 0.7747 (ttt180) REVERT: k 80 ASP cc_start: 0.8646 (m-30) cc_final: 0.8434 (m-30) REVERT: k 98 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7804 (ttp-110) REVERT: k 115 ILE cc_start: 0.9430 (mm) cc_final: 0.9222 (tp) REVERT: l 55 MET cc_start: 0.8339 (mmp) cc_final: 0.7921 (mmp) REVERT: l 57 LEU cc_start: 0.8928 (tp) cc_final: 0.8699 (tp) REVERT: l 59 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7539 (mtp85) REVERT: m 33 LEU cc_start: 0.6587 (tp) cc_final: 0.6276 (tt) REVERT: m 81 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6260 (mtt180) REVERT: m 106 ASP cc_start: 0.8932 (p0) cc_final: 0.8645 (p0) REVERT: m 111 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7931 (tp30) REVERT: n 17 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: n 73 ASN cc_start: 0.8469 (m-40) cc_final: 0.7971 (m-40) REVERT: n 110 MET cc_start: 0.8351 (mtm) cc_final: 0.8146 (mtm) REVERT: o 4 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8385 (mmmt) REVERT: o 17 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7938 (mmtm) REVERT: o 38 GLN cc_start: 0.7786 (pt0) cc_final: 0.6879 (pm20) REVERT: o 89 ASP cc_start: 0.8359 (m-30) cc_final: 0.8028 (m-30) REVERT: p 7 LEU cc_start: 0.8579 (tp) cc_final: 0.8285 (tp) REVERT: p 10 GLU cc_start: 0.7727 (mp0) cc_final: 0.7405 (mp0) REVERT: p 110 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8053 (mmtt) REVERT: q 4 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8089 (mtmt) REVERT: q 16 ILE cc_start: 0.8091 (mt) cc_final: 0.7847 (mt) REVERT: q 80 ASN cc_start: 0.8611 (t0) cc_final: 0.8371 (t0) REVERT: q 83 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8106 (ttpt) REVERT: q 93 ILE cc_start: 0.8887 (mm) cc_final: 0.8489 (mm) REVERT: r 13 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.7702 (tpt-90) REVERT: r 35 PHE cc_start: 0.8687 (m-80) cc_final: 0.8451 (m-80) REVERT: s 31 GLN cc_start: 0.7953 (tt0) cc_final: 0.7660 (tt0) REVERT: s 68 ASP cc_start: 0.9077 (t0) cc_final: 0.8301 (t70) REVERT: s 109 ASP cc_start: 0.7490 (p0) cc_final: 0.5819 (t0) REVERT: t 1 MET cc_start: 0.2027 (mtt) cc_final: 0.1784 (mtt) REVERT: t 11 LEU cc_start: 0.8135 (mt) cc_final: 0.7700 (mt) REVERT: t 37 ASP cc_start: 0.7158 (p0) cc_final: 0.6931 (p0) REVERT: u 39 ASN cc_start: 0.8173 (m-40) cc_final: 0.7488 (m110) REVERT: u 64 ILE cc_start: 0.7484 (tt) cc_final: 0.7164 (tt) REVERT: u 65 GLN cc_start: 0.8345 (mp10) cc_final: 0.7832 (mp10) REVERT: u 68 ASN cc_start: 0.7544 (m110) cc_final: 0.5876 (m110) REVERT: u 76 THR cc_start: 0.5637 (p) cc_final: 0.4800 (p) REVERT: u 78 LYS cc_start: 0.8814 (pttm) cc_final: 0.8505 (pttm) REVERT: w 21 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.7868 (mmm-85) REVERT: w 51 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7932 (ptm-80) REVERT: w 58 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7772 (mtpp) REVERT: w 60 ASP cc_start: 0.8768 (t0) cc_final: 0.8485 (t0) REVERT: x 43 LYS cc_start: 0.8299 (tmtt) cc_final: 0.8021 (tmmt) REVERT: y 26 PHE cc_start: 0.8409 (t80) cc_final: 0.7912 (t80) REVERT: y 30 MET cc_start: 0.8433 (mtm) cc_final: 0.8232 (mtm) REVERT: F 2 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7097 (mtpt) REVERT: F 34 LYS cc_start: 0.8051 (mttt) cc_final: 0.7829 (mtmt) REVERT: F 35 GLN cc_start: 0.7216 (pt0) cc_final: 0.6732 (pm20) REVERT: G 7 ASP cc_start: 0.9181 (t0) cc_final: 0.8925 (t0) REVERT: G 8 MET cc_start: 0.8354 (mpp) cc_final: 0.7985 (mpp) REVERT: G 21 TYR cc_start: 0.6909 (m-10) cc_final: 0.6477 (m-10) REVERT: G 22 TRP cc_start: 0.6602 (p-90) cc_final: 0.5957 (p-90) REVERT: G 57 ASN cc_start: 0.8787 (t0) cc_final: 0.8458 (m-40) REVERT: G 121 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8941 (mm-40) REVERT: G 132 GLU cc_start: 0.5662 (mm-30) cc_final: 0.5250 (tp30) REVERT: G 136 ARG cc_start: 0.7166 (mmm160) cc_final: 0.6661 (ttt90) REVERT: G 151 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8333 (mmmt) REVERT: G 172 ILE cc_start: 0.8284 (mm) cc_final: 0.8067 (mm) REVERT: G 212 TYR cc_start: 0.8787 (m-10) cc_final: 0.8365 (m-80) REVERT: H 33 ASP cc_start: 0.8096 (t0) cc_final: 0.7786 (t0) REVERT: H 69 THR cc_start: 0.7138 (p) cc_final: 0.6824 (t) REVERT: H 123 LEU cc_start: 0.9621 (mt) cc_final: 0.9350 (mt) REVERT: H 160 GLU cc_start: 0.6894 (pt0) cc_final: 0.6650 (pt0) REVERT: H 169 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7458 (tm-30) REVERT: H 200 TRP cc_start: 0.8355 (m100) cc_final: 0.7720 (m100) REVERT: I 13 ARG cc_start: 0.5173 (tpp-160) cc_final: 0.4649 (tpt170) REVERT: I 50 TYR cc_start: 0.7395 (t80) cc_final: 0.7076 (t80) REVERT: I 53 GLN cc_start: 0.8170 (pt0) cc_final: 0.7819 (pt0) REVERT: I 76 LYS cc_start: 0.5989 (mptt) cc_final: 0.5474 (mptt) REVERT: J 47 PHE cc_start: 0.8753 (p90) cc_final: 0.8493 (p90) REVERT: J 60 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7872 (tm-30) REVERT: J 64 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8502 (mt-10) REVERT: J 70 MET cc_start: 0.7727 (mtp) cc_final: 0.7079 (mtt) REVERT: J 127 TYR cc_start: 0.5909 (m-80) cc_final: 0.5363 (m-80) REVERT: J 146 MET cc_start: 0.7845 (mmm) cc_final: 0.7402 (mmm) REVERT: J 151 MET cc_start: 0.8395 (mmt) cc_final: 0.8092 (mmp) REVERT: K 23 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8818 (mp0) REVERT: K 40 GLU cc_start: 0.7624 (tt0) cc_final: 0.7038 (tp30) REVERT: K 72 ASP cc_start: 0.9147 (m-30) cc_final: 0.8858 (p0) REVERT: L 4 ARG cc_start: 0.4632 (mmt180) cc_final: 0.4360 (mmt180) REVERT: L 47 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8534 (tm-30) REVERT: L 48 THR cc_start: 0.8732 (p) cc_final: 0.8415 (p) REVERT: L 49 LEU cc_start: 0.9315 (pp) cc_final: 0.9010 (mm) REVERT: L 121 ASN cc_start: 0.8507 (m-40) cc_final: 0.8023 (m-40) REVERT: L 125 ASP cc_start: 0.8535 (m-30) cc_final: 0.8286 (m-30) REVERT: M 2 MET cc_start: 0.6532 (tpt) cc_final: 0.6152 (tpt) REVERT: M 8 ASP cc_start: 0.8474 (m-30) cc_final: 0.7785 (m-30) REVERT: M 9 MET cc_start: 0.6756 (ttp) cc_final: 0.5656 (tmm) REVERT: M 17 GLN cc_start: 0.9022 (mm110) cc_final: 0.8806 (mm-40) REVERT: M 26 MET cc_start: 0.7360 (ptp) cc_final: 0.6346 (ptp) REVERT: M 57 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7152 (mp0) REVERT: M 87 ARG cc_start: 0.6777 (tpp80) cc_final: 0.5657 (tpp-160) REVERT: M 98 LEU cc_start: 0.8322 (pp) cc_final: 0.7645 (pp) REVERT: M 110 MET cc_start: 0.7219 (ptt) cc_final: 0.6637 (ptt) REVERT: M 111 THR cc_start: 0.7950 (p) cc_final: 0.7750 (p) REVERT: N 24 ASN cc_start: 0.9143 (t0) cc_final: 0.8926 (p0) REVERT: N 67 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7091 (tptp) REVERT: N 102 PHE cc_start: 0.8510 (m-10) cc_final: 0.7080 (m-10) REVERT: N 114 LYS cc_start: 0.7062 (mppt) cc_final: 0.6808 (mtpt) REVERT: O 15 HIS cc_start: 0.6778 (p-80) cc_final: 0.6377 (p-80) REVERT: O 66 GLU cc_start: 0.8146 (pp20) cc_final: 0.7507 (tm-30) REVERT: O 67 ILE cc_start: 0.7753 (tt) cc_final: 0.7539 (tt) REVERT: O 72 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.6365 (mmm160) REVERT: O 88 MET cc_start: 0.5166 (mmt) cc_final: 0.4137 (ppp) REVERT: R 21 ILE cc_start: 0.8471 (mp) cc_final: 0.7982 (mp) REVERT: R 70 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8545 (mtt-85) REVERT: R 74 MET cc_start: 0.8261 (ppp) cc_final: 0.7955 (ppp) REVERT: S 15 LEU cc_start: 0.8307 (tp) cc_final: 0.7965 (tp) REVERT: S 61 ASN cc_start: 0.8452 (t0) cc_final: 0.8151 (t0) REVERT: T 46 LYS cc_start: 0.7042 (mtmm) cc_final: 0.6735 (mmmt) REVERT: U 79 ASN cc_start: 0.8297 (p0) cc_final: 0.8051 (p0) REVERT: V 62 GLU cc_start: 0.6709 (tp30) cc_final: 0.6343 (tp30) REVERT: W 11 ARG cc_start: 0.3395 (ttt-90) cc_final: 0.2220 (ttt180) REVERT: W 51 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8346 (tp-100) REVERT: X 65 MET cc_start: 0.7549 (ptt) cc_final: 0.7226 (ptt) REVERT: Y 15 LYS cc_start: 0.9073 (pptt) cc_final: 0.8853 (pptt) REVERT: Y 30 PHE cc_start: 0.9002 (m-80) cc_final: 0.8425 (m-80) REVERT: Y 78 LEU cc_start: 0.9061 (mm) cc_final: 0.8764 (mm) REVERT: Z 18 PHE cc_start: 0.7628 (t80) cc_final: 0.7334 (t80) REVERT: Z 32 ARG cc_start: 0.7387 (mpt180) cc_final: 0.7142 (mpt180) REVERT: a 7 ARG cc_start: 0.6830 (tpt90) cc_final: 0.5976 (mtt180) REVERT: a 167 LYS cc_start: 0.9016 (mttt) cc_final: 0.8660 (mmtt) outliers start: 6 outliers final: 1 residues processed: 1470 average time/residue: 1.5558 time to fit residues: 3912.9328 Evaluate side-chains 1258 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1257 time to evaluate : 6.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 20.0000 chunk 920 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 599 optimal weight: 30.0000 chunk 252 optimal weight: 8.9990 chunk 1022 optimal weight: 20.0000 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 338 optimal weight: 40.0000 chunk 536 optimal weight: 5.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN q 55 GLN r 87 GLN r 91 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 78 GLN w 42 HIS x 22 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN K 17 GLN K 55 HIS M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS T 19 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 163139 Z= 0.339 Angle : 0.785 15.461 244082 Z= 0.397 Chirality : 0.042 0.377 31220 Planarity : 0.006 0.081 13080 Dihedral : 23.963 179.136 81722 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.25 % Favored : 87.65 % Rotamer: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.10), residues: 5919 helix: -1.43 (0.11), residues: 1794 sheet: -2.27 (0.16), residues: 889 loop : -2.65 (0.10), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP e 96 HIS 0.015 0.002 HIS b 231 PHE 0.042 0.003 PHE g 29 TYR 0.069 0.003 TYR M 127 ARG 0.023 0.001 ARG o 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1467 time to evaluate : 6.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 193 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6408 (tm-30) REVERT: b 200 MET cc_start: 0.8105 (ptt) cc_final: 0.7564 (tmm) REVERT: b 212 TRP cc_start: 0.8324 (p90) cc_final: 0.7813 (p90) REVERT: b 269 ARG cc_start: 0.7441 (ttt90) cc_final: 0.7134 (ttt90) REVERT: c 82 PHE cc_start: 0.8190 (m-10) cc_final: 0.7899 (m-10) REVERT: c 175 LEU cc_start: 0.7976 (mt) cc_final: 0.7634 (mt) REVERT: c 188 LEU cc_start: 0.8360 (mt) cc_final: 0.8100 (mt) REVERT: c 200 ASP cc_start: 0.8140 (m-30) cc_final: 0.7857 (m-30) REVERT: d 25 GLU cc_start: 0.7176 (tt0) cc_final: 0.6745 (tt0) REVERT: d 51 GLU cc_start: 0.8083 (tt0) cc_final: 0.7867 (tt0) REVERT: d 99 LYS cc_start: 0.5953 (mttt) cc_final: 0.5616 (ttpp) REVERT: d 111 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7194 (tm-30) REVERT: d 136 GLN cc_start: 0.7604 (pp30) cc_final: 0.7392 (pp30) REVERT: d 188 MET cc_start: 0.5481 (ptp) cc_final: 0.5049 (ptm) REVERT: e 19 PHE cc_start: 0.8411 (m-80) cc_final: 0.8195 (m-80) REVERT: e 21 TYR cc_start: 0.7963 (m-10) cc_final: 0.7418 (m-10) REVERT: e 32 LYS cc_start: 0.8896 (tmmt) cc_final: 0.8589 (tmtt) REVERT: e 82 TYR cc_start: 0.7806 (t80) cc_final: 0.7216 (t80) REVERT: e 89 THR cc_start: 0.8896 (p) cc_final: 0.8324 (p) REVERT: e 90 LEU cc_start: 0.9189 (tp) cc_final: 0.8681 (tp) REVERT: e 110 ILE cc_start: 0.9326 (mt) cc_final: 0.9096 (mm) REVERT: e 133 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6506 (mm-30) REVERT: e 174 PHE cc_start: 0.6526 (m-80) cc_final: 0.6235 (m-80) REVERT: f 21 GLN cc_start: 0.8504 (pm20) cc_final: 0.8295 (pm20) REVERT: f 41 GLU cc_start: 0.8915 (tt0) cc_final: 0.8225 (tm-30) REVERT: f 54 ARG cc_start: 0.8524 (ttm110) cc_final: 0.7977 (ttm110) REVERT: f 127 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7597 (mm-40) REVERT: f 133 LYS cc_start: 0.7315 (tptt) cc_final: 0.6977 (tppt) REVERT: g 1 MET cc_start: 0.8106 (tpp) cc_final: 0.7894 (tpp) REVERT: g 7 ASP cc_start: 0.6788 (p0) cc_final: 0.6286 (p0) REVERT: g 29 PHE cc_start: 0.8248 (t80) cc_final: 0.7916 (t80) REVERT: i 124 MET cc_start: -0.4308 (ptp) cc_final: -0.4727 (mmm) REVERT: i 135 MET cc_start: 0.5665 (ptp) cc_final: 0.5221 (mmt) REVERT: j 31 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7445 (mm-30) REVERT: j 41 LYS cc_start: 0.8833 (mttt) cc_final: 0.8454 (mttt) REVERT: j 71 ASP cc_start: 0.8417 (m-30) cc_final: 0.7798 (m-30) REVERT: j 106 LYS cc_start: 0.8245 (tptt) cc_final: 0.7823 (tptt) REVERT: j 118 MET cc_start: 0.8867 (ptp) cc_final: 0.8626 (ptp) REVERT: j 132 HIS cc_start: 0.7316 (m-70) cc_final: 0.7039 (m-70) REVERT: k 2 ILE cc_start: 0.7910 (mm) cc_final: 0.7450 (mm) REVERT: k 20 MET cc_start: 0.7746 (tpt) cc_final: 0.7492 (tpt) REVERT: k 29 HIS cc_start: 0.8490 (t70) cc_final: 0.8108 (t70) REVERT: k 80 ASP cc_start: 0.8677 (m-30) cc_final: 0.8233 (m-30) REVERT: k 114 LYS cc_start: 0.8667 (tptm) cc_final: 0.8436 (tppp) REVERT: k 115 ILE cc_start: 0.9443 (mm) cc_final: 0.9188 (tp) REVERT: l 55 MET cc_start: 0.8360 (mmp) cc_final: 0.7925 (mmp) REVERT: l 59 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7526 (mtp85) REVERT: m 33 LEU cc_start: 0.6507 (tp) cc_final: 0.6291 (tt) REVERT: m 81 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6510 (mtt180) REVERT: m 106 ASP cc_start: 0.9056 (p0) cc_final: 0.8798 (p0) REVERT: m 111 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7986 (tp30) REVERT: n 17 ARG cc_start: 0.8722 (ttp-110) cc_final: 0.8366 (ttp-110) REVERT: n 20 MET cc_start: 0.7627 (tpt) cc_final: 0.7413 (tpp) REVERT: n 24 MET cc_start: 0.7699 (mtp) cc_final: 0.7297 (mtt) REVERT: n 65 LEU cc_start: 0.8763 (tt) cc_final: 0.8159 (tt) REVERT: n 69 ARG cc_start: 0.8234 (mpt-90) cc_final: 0.8013 (mmt90) REVERT: n 73 ASN cc_start: 0.8552 (m-40) cc_final: 0.8108 (m-40) REVERT: o 4 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8399 (mmmt) REVERT: o 38 GLN cc_start: 0.7967 (pt0) cc_final: 0.6930 (pm20) REVERT: o 89 ASP cc_start: 0.8163 (m-30) cc_final: 0.7685 (m-30) REVERT: p 10 GLU cc_start: 0.7740 (mp0) cc_final: 0.7508 (mp0) REVERT: p 43 GLU cc_start: 0.7356 (tp30) cc_final: 0.6949 (tp30) REVERT: p 61 ARG cc_start: 0.8468 (ttt90) cc_final: 0.8259 (ttt90) REVERT: p 105 LYS cc_start: 0.8937 (tptp) cc_final: 0.8468 (tptm) REVERT: q 4 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8108 (mtmt) REVERT: q 16 ILE cc_start: 0.8127 (mt) cc_final: 0.7904 (mt) REVERT: q 93 ILE cc_start: 0.8841 (mm) cc_final: 0.8463 (mm) REVERT: r 11 GLN cc_start: 0.8395 (mp10) cc_final: 0.8055 (mp10) REVERT: r 13 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.8126 (ttt-90) REVERT: r 35 PHE cc_start: 0.8608 (m-80) cc_final: 0.8404 (m-80) REVERT: s 31 GLN cc_start: 0.8027 (tt0) cc_final: 0.7728 (tt0) REVERT: s 68 ASP cc_start: 0.9107 (t0) cc_final: 0.8398 (t0) REVERT: s 78 GLU cc_start: 0.7330 (tp30) cc_final: 0.6912 (tp30) REVERT: s 99 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7772 (mtp-110) REVERT: s 109 ASP cc_start: 0.7539 (p0) cc_final: 0.5862 (t0) REVERT: t 11 LEU cc_start: 0.8125 (mt) cc_final: 0.7710 (mt) REVERT: u 6 ARG cc_start: 0.6668 (ttp-170) cc_final: 0.6342 (ttp-170) REVERT: u 39 ASN cc_start: 0.8057 (m-40) cc_final: 0.7416 (m110) REVERT: u 64 ILE cc_start: 0.7664 (tt) cc_final: 0.7324 (tt) REVERT: u 65 GLN cc_start: 0.8331 (mp10) cc_final: 0.7796 (mp10) REVERT: u 68 ASN cc_start: 0.7469 (m110) cc_final: 0.5753 (m110) REVERT: v 76 ASP cc_start: 0.8175 (m-30) cc_final: 0.7877 (m-30) REVERT: w 21 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.7771 (mmm-85) REVERT: w 25 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7005 (mt-10) REVERT: w 51 ARG cc_start: 0.8012 (ptm-80) cc_final: 0.7605 (ptm-80) REVERT: w 60 ASP cc_start: 0.8748 (t0) cc_final: 0.8487 (t0) REVERT: x 24 THR cc_start: 0.6829 (m) cc_final: 0.6599 (m) REVERT: y 26 PHE cc_start: 0.8346 (t80) cc_final: 0.8068 (t80) REVERT: y 29 ARG cc_start: 0.8425 (ttt-90) cc_final: 0.8142 (ttt-90) REVERT: B 9 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7078 (mtp85) REVERT: B 11 LYS cc_start: 0.7703 (tppp) cc_final: 0.7499 (ttmt) REVERT: C 37 LYS cc_start: 0.7516 (tppt) cc_final: 0.7222 (mmtm) REVERT: F 2 LYS cc_start: 0.7510 (mmmt) cc_final: 0.7157 (mtpt) REVERT: F 24 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7205 (mtt-85) REVERT: F 34 LYS cc_start: 0.8073 (mttt) cc_final: 0.7866 (mttt) REVERT: F 35 GLN cc_start: 0.7205 (pt0) cc_final: 0.6771 (pm20) REVERT: G 7 ASP cc_start: 0.9235 (t0) cc_final: 0.9031 (t0) REVERT: G 8 MET cc_start: 0.8325 (mpp) cc_final: 0.7976 (mpp) REVERT: G 21 TYR cc_start: 0.6829 (m-10) cc_final: 0.6416 (m-10) REVERT: G 22 TRP cc_start: 0.6736 (p-90) cc_final: 0.6214 (p-90) REVERT: G 57 ASN cc_start: 0.8742 (t0) cc_final: 0.8502 (m-40) REVERT: G 121 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8949 (mm-40) REVERT: G 132 GLU cc_start: 0.5272 (mm-30) cc_final: 0.4750 (tp30) REVERT: G 136 ARG cc_start: 0.7166 (mmm160) cc_final: 0.6728 (ttt90) REVERT: G 151 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8464 (mmmt) REVERT: G 212 TYR cc_start: 0.8782 (m-10) cc_final: 0.8383 (m-80) REVERT: H 27 GLU cc_start: 0.7943 (mp0) cc_final: 0.7372 (pm20) REVERT: H 33 ASP cc_start: 0.8098 (t0) cc_final: 0.7764 (t0) REVERT: H 54 ILE cc_start: 0.8741 (pt) cc_final: 0.7014 (pt) REVERT: H 69 THR cc_start: 0.7264 (p) cc_final: 0.6864 (t) REVERT: H 81 GLU cc_start: 0.9145 (mp0) cc_final: 0.8794 (mp0) REVERT: H 104 GLU cc_start: 0.7584 (pp20) cc_final: 0.7102 (pp20) REVERT: H 160 GLU cc_start: 0.6847 (pt0) cc_final: 0.6634 (pt0) REVERT: H 169 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 200 TRP cc_start: 0.8682 (m100) cc_final: 0.8317 (m100) REVERT: I 13 ARG cc_start: 0.5163 (tpp-160) cc_final: 0.4644 (tpt170) REVERT: I 50 TYR cc_start: 0.7359 (t80) cc_final: 0.6940 (t80) REVERT: I 53 GLN cc_start: 0.8049 (pt0) cc_final: 0.7734 (pt0) REVERT: I 64 TYR cc_start: 0.6208 (m-80) cc_final: 0.5867 (m-10) REVERT: I 76 LYS cc_start: 0.5756 (mptt) cc_final: 0.5191 (mptt) REVERT: I 104 MET cc_start: 0.3134 (mmp) cc_final: 0.2906 (mmm) REVERT: J 63 MET cc_start: 0.8465 (ptt) cc_final: 0.8118 (ptt) REVERT: J 70 MET cc_start: 0.7750 (mtp) cc_final: 0.7240 (mtt) REVERT: J 127 TYR cc_start: 0.6370 (m-80) cc_final: 0.5883 (m-80) REVERT: J 134 ASN cc_start: 0.6516 (t0) cc_final: 0.5886 (t0) REVERT: J 146 MET cc_start: 0.7777 (mmm) cc_final: 0.7533 (mmm) REVERT: K 40 GLU cc_start: 0.7633 (tt0) cc_final: 0.7094 (tp30) REVERT: K 72 ASP cc_start: 0.9131 (m-30) cc_final: 0.8794 (p0) REVERT: L 4 ARG cc_start: 0.4735 (mmt180) cc_final: 0.4358 (mmt180) REVERT: L 47 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8582 (tm-30) REVERT: L 48 THR cc_start: 0.8656 (p) cc_final: 0.8215 (p) REVERT: L 49 LEU cc_start: 0.9237 (pp) cc_final: 0.8964 (mm) REVERT: L 51 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8524 (mm-40) REVERT: L 115 MET cc_start: 0.6497 (tpp) cc_final: 0.6140 (tpp) REVERT: L 121 ASN cc_start: 0.8476 (m-40) cc_final: 0.8181 (m110) REVERT: L 125 ASP cc_start: 0.8505 (m-30) cc_final: 0.8195 (m-30) REVERT: M 2 MET cc_start: 0.6561 (tpt) cc_final: 0.6317 (tpt) REVERT: M 8 ASP cc_start: 0.8521 (m-30) cc_final: 0.7732 (m-30) REVERT: M 9 MET cc_start: 0.6429 (ttp) cc_final: 0.5497 (tmm) REVERT: M 26 MET cc_start: 0.7552 (ptp) cc_final: 0.6615 (ptp) REVERT: M 35 ILE cc_start: 0.9224 (pt) cc_final: 0.8994 (pt) REVERT: M 57 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7160 (mp0) REVERT: M 77 VAL cc_start: 0.5440 (t) cc_final: 0.4926 (t) REVERT: M 87 ARG cc_start: 0.6778 (tpp80) cc_final: 0.5566 (tpp-160) REVERT: M 98 LEU cc_start: 0.8363 (pp) cc_final: 0.8005 (pp) REVERT: N 24 ASN cc_start: 0.9162 (t0) cc_final: 0.8640 (t0) REVERT: N 45 MET cc_start: 0.8935 (mmp) cc_final: 0.8724 (mmm) REVERT: N 67 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7085 (tptp) REVERT: O 66 GLU cc_start: 0.8241 (pp20) cc_final: 0.7558 (tm-30) REVERT: O 67 ILE cc_start: 0.7761 (tt) cc_final: 0.7544 (tt) REVERT: P 118 ASN cc_start: 0.8418 (t0) cc_final: 0.6694 (p0) REVERT: R 2 ARG cc_start: 0.6046 (tpt170) cc_final: 0.5650 (tpt-90) REVERT: R 70 ARG cc_start: 0.9036 (mtt180) cc_final: 0.8629 (mtt-85) REVERT: R 74 MET cc_start: 0.8205 (ppp) cc_final: 0.7903 (ppp) REVERT: R 76 ILE cc_start: 0.9358 (pt) cc_final: 0.9153 (pt) REVERT: S 15 LEU cc_start: 0.8387 (tp) cc_final: 0.8049 (tp) REVERT: S 61 ASN cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) REVERT: T 10 ILE cc_start: 0.9006 (mp) cc_final: 0.8779 (mp) REVERT: T 46 LYS cc_start: 0.7059 (mtmm) cc_final: 0.6760 (mmmm) REVERT: U 31 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7738 (mmt90) REVERT: U 79 ASN cc_start: 0.8343 (p0) cc_final: 0.8100 (p0) REVERT: V 62 GLU cc_start: 0.6746 (tp30) cc_final: 0.6352 (tp30) REVERT: V 72 TRP cc_start: 0.8642 (m100) cc_final: 0.8413 (m100) REVERT: W 51 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8106 (tp-100) REVERT: X 65 MET cc_start: 0.7651 (ptt) cc_final: 0.7292 (ptt) REVERT: Y 15 LYS cc_start: 0.9119 (pptt) cc_final: 0.8840 (pptt) REVERT: Y 30 PHE cc_start: 0.8880 (m-80) cc_final: 0.8341 (m-80) REVERT: Y 78 LEU cc_start: 0.8964 (mm) cc_final: 0.8631 (mm) REVERT: Z 18 PHE cc_start: 0.7703 (t80) cc_final: 0.7276 (t80) REVERT: a 7 ARG cc_start: 0.6780 (tpt90) cc_final: 0.5975 (mtt180) REVERT: a 167 LYS cc_start: 0.9041 (mttt) cc_final: 0.8699 (mmtt) REVERT: a 218 MET cc_start: 0.6789 (tpt) cc_final: 0.6253 (tpt) outliers start: 3 outliers final: 0 residues processed: 1469 average time/residue: 1.3854 time to fit residues: 3438.7529 Evaluate side-chains 1260 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1260 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 582 optimal weight: 10.0000 chunk 746 optimal weight: 20.0000 chunk 578 optimal weight: 50.0000 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 40.0000 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 621 optimal weight: 20.0000 chunk 470 optimal weight: 20.0000 overall best weight: 12.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 225 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 195 GLN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 60 GLN ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN q 80 ASN r 87 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN x 22 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS U 26 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 HIS ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 163139 Z= 0.536 Angle : 1.046 18.318 244082 Z= 0.517 Chirality : 0.053 0.330 31220 Planarity : 0.008 0.167 13080 Dihedral : 24.533 178.218 81722 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 42.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.63 % Favored : 84.22 % Rotamer: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.10), residues: 5919 helix: -1.95 (0.11), residues: 1757 sheet: -2.43 (0.16), residues: 847 loop : -2.91 (0.10), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP b 212 HIS 0.016 0.003 HIS T 45 PHE 0.072 0.004 PHE G 89 TYR 0.051 0.004 TYR Q 65 ARG 0.032 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1422 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 24 HIS cc_start: 0.6777 (t-170) cc_final: 0.6153 (t-170) REVERT: b 81 GLU cc_start: 0.7951 (tp30) cc_final: 0.7658 (tp30) REVERT: b 82 TYR cc_start: 0.7522 (t80) cc_final: 0.7243 (t80) REVERT: b 99 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7557 (mm-30) REVERT: b 200 MET cc_start: 0.8038 (ptt) cc_final: 0.7779 (tmm) REVERT: b 212 TRP cc_start: 0.8421 (p90) cc_final: 0.7835 (p90) REVERT: b 257 ARG cc_start: 0.7295 (tpt-90) cc_final: 0.5440 (tpt-90) REVERT: b 259 ASN cc_start: 0.8147 (m110) cc_final: 0.7676 (m-40) REVERT: d 25 GLU cc_start: 0.7403 (tt0) cc_final: 0.6975 (tt0) REVERT: d 51 GLU cc_start: 0.8144 (tt0) cc_final: 0.7679 (tt0) REVERT: d 74 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8607 (ttmt) REVERT: d 111 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7045 (tm-30) REVERT: d 136 GLN cc_start: 0.7991 (pp30) cc_final: 0.7760 (pp30) REVERT: d 183 PHE cc_start: 0.6394 (m-80) cc_final: 0.5317 (m-80) REVERT: d 184 ASP cc_start: 0.7979 (m-30) cc_final: 0.7423 (m-30) REVERT: d 188 MET cc_start: 0.5627 (ptp) cc_final: 0.5113 (ptm) REVERT: e 19 PHE cc_start: 0.8415 (m-80) cc_final: 0.8198 (m-80) REVERT: e 21 TYR cc_start: 0.8437 (m-10) cc_final: 0.7572 (m-10) REVERT: e 82 TYR cc_start: 0.7853 (t80) cc_final: 0.6993 (t80) REVERT: e 89 THR cc_start: 0.8798 (p) cc_final: 0.8153 (p) REVERT: e 90 LEU cc_start: 0.9155 (tp) cc_final: 0.8583 (tp) REVERT: e 172 PHE cc_start: 0.7810 (m-80) cc_final: 0.7477 (m-80) REVERT: e 174 PHE cc_start: 0.6983 (m-80) cc_final: 0.6706 (m-80) REVERT: f 41 GLU cc_start: 0.8931 (tt0) cc_final: 0.8523 (tm-30) REVERT: f 71 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (pp) REVERT: f 133 LYS cc_start: 0.7334 (tptt) cc_final: 0.6986 (tppt) REVERT: g 8 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8757 (tptp) REVERT: i 124 MET cc_start: -0.3787 (ptp) cc_final: -0.4255 (mmm) REVERT: i 135 MET cc_start: 0.5664 (ptp) cc_final: 0.5231 (mmt) REVERT: j 41 LYS cc_start: 0.8786 (mttt) cc_final: 0.8511 (mttt) REVERT: j 44 TYR cc_start: 0.8623 (t80) cc_final: 0.8380 (t80) REVERT: j 67 ASN cc_start: 0.7712 (t0) cc_final: 0.7505 (t0) REVERT: j 71 ASP cc_start: 0.8782 (m-30) cc_final: 0.8345 (m-30) REVERT: j 95 ARG cc_start: 0.7878 (mpt180) cc_final: 0.7585 (mmt180) REVERT: j 118 MET cc_start: 0.8950 (ptp) cc_final: 0.8716 (ptp) REVERT: k 29 HIS cc_start: 0.8456 (t70) cc_final: 0.8059 (t70) REVERT: k 71 ARG cc_start: 0.8170 (tpt-90) cc_final: 0.7954 (ttt180) REVERT: k 80 ASP cc_start: 0.8481 (m-30) cc_final: 0.8204 (m-30) REVERT: l 55 MET cc_start: 0.8373 (mmp) cc_final: 0.7911 (mmp) REVERT: l 59 ARG cc_start: 0.8499 (mtp85) cc_final: 0.7721 (mtp85) REVERT: m 81 ARG cc_start: 0.7470 (mtt180) cc_final: 0.6837 (mtt180) REVERT: m 106 ASP cc_start: 0.9097 (p0) cc_final: 0.8764 (p0) REVERT: m 111 GLU cc_start: 0.8711 (tp30) cc_final: 0.8346 (tp30) REVERT: n 4 ARG cc_start: 0.7774 (mmt180) cc_final: 0.7110 (mmm160) REVERT: n 17 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8274 (ttp-110) REVERT: n 24 MET cc_start: 0.7591 (mtp) cc_final: 0.7142 (mtt) REVERT: n 46 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8324 (ttm110) REVERT: n 62 ASN cc_start: 0.8474 (m-40) cc_final: 0.8242 (m-40) REVERT: n 65 LEU cc_start: 0.8698 (tt) cc_final: 0.8287 (tt) REVERT: n 73 ASN cc_start: 0.8611 (m-40) cc_final: 0.8276 (m-40) REVERT: n 106 ASP cc_start: 0.8006 (p0) cc_final: 0.7788 (p0) REVERT: o 4 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8467 (mmmt) REVERT: o 17 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8096 (mmtt) REVERT: o 98 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6137 (mm110) REVERT: p 6 GLN cc_start: 0.7969 (tt0) cc_final: 0.7580 (tt0) REVERT: p 10 GLU cc_start: 0.7666 (mp0) cc_final: 0.6951 (mp0) REVERT: p 43 GLU cc_start: 0.7538 (tp30) cc_final: 0.7237 (tp30) REVERT: p 52 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7725 (mmm160) REVERT: p 92 ARG cc_start: 0.6586 (mmt180) cc_final: 0.5925 (mmt180) REVERT: p 105 LYS cc_start: 0.8995 (tppt) cc_final: 0.8443 (tppp) REVERT: q 4 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8230 (mtmt) REVERT: q 16 ILE cc_start: 0.8470 (mt) cc_final: 0.8139 (mt) REVERT: r 35 PHE cc_start: 0.8852 (m-80) cc_final: 0.8614 (m-80) REVERT: r 49 ILE cc_start: 0.7291 (pt) cc_final: 0.7084 (pt) REVERT: s 31 GLN cc_start: 0.8097 (tt0) cc_final: 0.7759 (tt0) REVERT: s 68 ASP cc_start: 0.9067 (t0) cc_final: 0.8470 (t70) REVERT: s 78 GLU cc_start: 0.7525 (tp30) cc_final: 0.6590 (tp30) REVERT: s 99 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7461 (mtp85) REVERT: s 109 ASP cc_start: 0.7774 (p0) cc_final: 0.6147 (t0) REVERT: t 11 LEU cc_start: 0.8233 (mt) cc_final: 0.7825 (mt) REVERT: t 89 GLU cc_start: 0.8981 (mm-30) cc_final: 0.7837 (tm-30) REVERT: u 34 ILE cc_start: 0.8527 (mt) cc_final: 0.8259 (mt) REVERT: u 39 ASN cc_start: 0.8185 (m-40) cc_final: 0.7544 (m110) REVERT: u 64 ILE cc_start: 0.7686 (tt) cc_final: 0.7409 (tt) REVERT: u 65 GLN cc_start: 0.8366 (mp10) cc_final: 0.7868 (mp10) REVERT: u 68 ASN cc_start: 0.7563 (m110) cc_final: 0.6189 (m110) REVERT: v 46 LYS cc_start: 0.9696 (mtpt) cc_final: 0.9354 (mtmm) REVERT: v 48 MET cc_start: 0.8366 (tmm) cc_final: 0.8033 (tpt) REVERT: v 50 MET cc_start: 0.9005 (mtp) cc_final: 0.8646 (mtp) REVERT: v 76 ASP cc_start: 0.8228 (m-30) cc_final: 0.7862 (m-30) REVERT: w 25 GLU cc_start: 0.8111 (mt-10) cc_final: 0.6914 (mt-10) REVERT: w 58 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7864 (mtpp) REVERT: w 60 ASP cc_start: 0.8827 (t0) cc_final: 0.8549 (t0) REVERT: y 26 PHE cc_start: 0.8516 (t80) cc_final: 0.8227 (t80) REVERT: z 55 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8338 (tptt) REVERT: z 57 GLU cc_start: 0.6388 (tm-30) cc_final: 0.6104 (tm-30) REVERT: D 13 ASN cc_start: 0.8376 (m-40) cc_final: 0.7824 (m110) REVERT: E 29 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8106 (mmt-90) REVERT: E 51 LYS cc_start: 0.7029 (ptmm) cc_final: 0.6801 (ttpp) REVERT: G 8 MET cc_start: 0.8300 (mpp) cc_final: 0.8031 (mpp) REVERT: G 18 GLN cc_start: 0.6034 (pm20) cc_final: 0.5661 (pm20) REVERT: G 21 TYR cc_start: 0.7282 (m-10) cc_final: 0.6876 (m-10) REVERT: G 22 TRP cc_start: 0.6742 (p-90) cc_final: 0.6191 (p-90) REVERT: G 92 ASN cc_start: 0.9234 (p0) cc_final: 0.9006 (p0) REVERT: G 121 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8987 (mm-40) REVERT: G 151 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8596 (mmmt) REVERT: G 164 ASP cc_start: 0.9070 (t0) cc_final: 0.8752 (t0) REVERT: G 212 TYR cc_start: 0.8756 (m-10) cc_final: 0.8299 (m-80) REVERT: H 69 THR cc_start: 0.7386 (p) cc_final: 0.7050 (t) REVERT: H 122 GLN cc_start: 0.8857 (pp30) cc_final: 0.8642 (pm20) REVERT: H 151 GLU cc_start: 0.7719 (mp0) cc_final: 0.6353 (mp0) REVERT: H 169 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7737 (tm-30) REVERT: H 200 TRP cc_start: 0.8573 (m100) cc_final: 0.7551 (m100) REVERT: I 13 ARG cc_start: 0.5297 (tpp-160) cc_final: 0.4886 (tpt90) REVERT: I 50 TYR cc_start: 0.7416 (t80) cc_final: 0.6926 (t80) REVERT: I 64 TYR cc_start: 0.5864 (m-80) cc_final: 0.5627 (m-80) REVERT: I 104 MET cc_start: 0.3228 (mmp) cc_final: 0.3017 (mmm) REVERT: J 70 MET cc_start: 0.7579 (mtp) cc_final: 0.6349 (mtp) REVERT: K 21 MET cc_start: 0.9009 (mtp) cc_final: 0.8687 (mtt) REVERT: K 40 GLU cc_start: 0.8158 (tt0) cc_final: 0.7018 (tp30) REVERT: K 90 MET cc_start: 0.7849 (mmp) cc_final: 0.7622 (mmp) REVERT: L 47 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8523 (tm-30) REVERT: L 51 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8609 (mm-40) REVERT: L 115 MET cc_start: 0.6651 (tpp) cc_final: 0.6343 (tpp) REVERT: L 121 ASN cc_start: 0.8467 (m-40) cc_final: 0.8226 (m110) REVERT: L 125 ASP cc_start: 0.8523 (m-30) cc_final: 0.8212 (m-30) REVERT: M 9 MET cc_start: 0.6550 (ttp) cc_final: 0.5553 (tmm) REVERT: M 26 MET cc_start: 0.7389 (ptp) cc_final: 0.6454 (ptp) REVERT: M 57 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7199 (mp0) REVERT: M 87 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6206 (tpp-160) REVERT: M 110 MET cc_start: 0.7443 (ptt) cc_final: 0.6829 (ptt) REVERT: N 24 ASN cc_start: 0.9326 (t0) cc_final: 0.8836 (t0) REVERT: N 67 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7139 (tptp) REVERT: O 66 GLU cc_start: 0.8225 (pp20) cc_final: 0.7635 (pp20) REVERT: O 67 ILE cc_start: 0.7742 (tt) cc_final: 0.7521 (tt) REVERT: Q 81 ILE cc_start: 0.7423 (tp) cc_final: 0.7149 (tp) REVERT: R 2 ARG cc_start: 0.6450 (tpt170) cc_final: 0.6129 (tpt-90) REVERT: R 22 TYR cc_start: 0.7792 (t80) cc_final: 0.7579 (t80) REVERT: R 70 ARG cc_start: 0.9103 (mtt180) cc_final: 0.8872 (mtp180) REVERT: R 74 MET cc_start: 0.8298 (ppp) cc_final: 0.7977 (ppp) REVERT: S 15 LEU cc_start: 0.8363 (tp) cc_final: 0.8053 (tp) REVERT: S 61 ASN cc_start: 0.8576 (t0) cc_final: 0.8315 (t0) REVERT: T 46 LYS cc_start: 0.7175 (mtmm) cc_final: 0.6865 (mmmm) REVERT: U 9 HIS cc_start: 0.5813 (m-70) cc_final: 0.5533 (m-70) REVERT: U 31 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7762 (mmt90) REVERT: U 79 ASN cc_start: 0.8475 (p0) cc_final: 0.8240 (p0) REVERT: V 72 TRP cc_start: 0.8768 (m100) cc_final: 0.8498 (m100) REVERT: W 51 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8173 (tp-100) REVERT: X 65 MET cc_start: 0.7692 (ptt) cc_final: 0.7190 (ptt) REVERT: Y 15 LYS cc_start: 0.9064 (pptt) cc_final: 0.8808 (pptt) REVERT: Y 30 PHE cc_start: 0.8947 (m-80) cc_final: 0.8390 (m-80) REVERT: Y 39 GLU cc_start: 0.8769 (mp0) cc_final: 0.8359 (mp0) REVERT: Y 42 ASP cc_start: 0.8557 (t0) cc_final: 0.8148 (t0) REVERT: Y 78 LEU cc_start: 0.9039 (mm) cc_final: 0.8685 (mm) REVERT: Z 18 PHE cc_start: 0.7801 (t80) cc_final: 0.7352 (t80) REVERT: a 7 ARG cc_start: 0.6956 (tpt90) cc_final: 0.6119 (mtt180) REVERT: a 167 LYS cc_start: 0.9134 (mttt) cc_final: 0.8854 (mttt) outliers start: 3 outliers final: 1 residues processed: 1424 average time/residue: 1.4500 time to fit residues: 3491.5865 Evaluate side-chains 1218 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1217 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 608 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 647 optimal weight: 10.0000 chunk 694 optimal weight: 40.0000 chunk 503 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 800 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN b 142 ASN b 196 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN d 97 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN q 80 ASN r 87 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 49 ASN v 78 GLN w 42 HIS ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS L 67 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS R 13 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 163139 Z= 0.223 Angle : 0.712 13.447 244082 Z= 0.364 Chirality : 0.039 0.322 31220 Planarity : 0.006 0.131 13080 Dihedral : 24.141 178.577 81722 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.98 % Favored : 88.92 % Rotamer: Outliers : 0.08 % Allowed : 1.61 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.10), residues: 5919 helix: -1.50 (0.11), residues: 1795 sheet: -2.17 (0.16), residues: 876 loop : -2.63 (0.10), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP b 212 HIS 0.014 0.002 HIS m 13 PHE 0.034 0.002 PHE G 89 TYR 0.021 0.002 TYR I 75 ARG 0.021 0.001 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1487 time to evaluate : 6.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 81 GLU cc_start: 0.8062 (tp30) cc_final: 0.7859 (tp30) REVERT: b 82 TYR cc_start: 0.7534 (t80) cc_final: 0.6986 (t80) REVERT: b 99 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7290 (mm-30) REVERT: b 131 MET cc_start: 0.9247 (mpp) cc_final: 0.8787 (mpp) REVERT: b 200 MET cc_start: 0.8160 (ptt) cc_final: 0.7493 (tmm) REVERT: b 257 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6559 (tpt-90) REVERT: c 1 MET cc_start: 0.8343 (mtm) cc_final: 0.8078 (mtm) REVERT: c 28 GLU cc_start: 0.6965 (tm-30) cc_final: 0.5993 (tm-30) REVERT: c 188 LEU cc_start: 0.8400 (mp) cc_final: 0.8128 (mp) REVERT: c 200 ASP cc_start: 0.8016 (m-30) cc_final: 0.7318 (m-30) REVERT: d 25 GLU cc_start: 0.6893 (tt0) cc_final: 0.6507 (tt0) REVERT: d 51 GLU cc_start: 0.7976 (tt0) cc_final: 0.7739 (tt0) REVERT: d 136 GLN cc_start: 0.7662 (pp30) cc_final: 0.7356 (pp30) REVERT: d 183 PHE cc_start: 0.6111 (m-80) cc_final: 0.5248 (m-80) REVERT: d 184 ASP cc_start: 0.7722 (m-30) cc_final: 0.7248 (m-30) REVERT: d 188 MET cc_start: 0.5286 (ptp) cc_final: 0.4885 (ptm) REVERT: d 194 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9207 (mmmt) REVERT: e 19 PHE cc_start: 0.8259 (m-80) cc_final: 0.8032 (m-80) REVERT: e 21 TYR cc_start: 0.8300 (m-10) cc_final: 0.7544 (m-10) REVERT: e 82 TYR cc_start: 0.7835 (t80) cc_final: 0.7209 (t80) REVERT: e 107 VAL cc_start: 0.9469 (t) cc_final: 0.9163 (t) REVERT: f 41 GLU cc_start: 0.8888 (tt0) cc_final: 0.8396 (tm-30) REVERT: f 127 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7552 (mm110) REVERT: f 133 LYS cc_start: 0.6884 (tptt) cc_final: 0.6560 (tppt) REVERT: g 7 ASP cc_start: 0.7463 (p0) cc_final: 0.6765 (p0) REVERT: g 8 LYS cc_start: 0.8949 (tmtt) cc_final: 0.8678 (tptp) REVERT: h 1 MET cc_start: 0.5705 (ppp) cc_final: 0.5371 (ppp) REVERT: i 124 MET cc_start: -0.4162 (ptp) cc_final: -0.4482 (mmm) REVERT: i 135 MET cc_start: 0.5586 (ptp) cc_final: 0.5184 (mmt) REVERT: j 31 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7298 (mm-30) REVERT: j 67 ASN cc_start: 0.7259 (t0) cc_final: 0.6884 (t0) REVERT: j 71 ASP cc_start: 0.8495 (m-30) cc_final: 0.7884 (m-30) REVERT: k 2 ILE cc_start: 0.7591 (mm) cc_final: 0.7003 (mm) REVERT: k 29 HIS cc_start: 0.8259 (t70) cc_final: 0.7901 (t70) REVERT: k 80 ASP cc_start: 0.8653 (m-30) cc_final: 0.8176 (m-30) REVERT: k 98 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8135 (ttm110) REVERT: l 55 MET cc_start: 0.8380 (mmp) cc_final: 0.7940 (mmp) REVERT: l 57 LEU cc_start: 0.9007 (tp) cc_final: 0.8716 (tp) REVERT: l 59 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7721 (mtp85) REVERT: l 103 ILE cc_start: 0.9012 (tp) cc_final: 0.8750 (tp) REVERT: m 53 MET cc_start: 0.6926 (ttm) cc_final: 0.6477 (tmm) REVERT: m 81 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6708 (mtt180) REVERT: m 106 ASP cc_start: 0.9044 (p0) cc_final: 0.8762 (p0) REVERT: m 111 GLU cc_start: 0.8720 (tp30) cc_final: 0.8495 (tp30) REVERT: n 24 MET cc_start: 0.7532 (mtp) cc_final: 0.7274 (mtt) REVERT: n 29 VAL cc_start: 0.8846 (t) cc_final: 0.8604 (p) REVERT: n 62 ASN cc_start: 0.8275 (m-40) cc_final: 0.8020 (m110) REVERT: n 73 ASN cc_start: 0.8452 (m-40) cc_final: 0.8071 (m-40) REVERT: n 110 MET cc_start: 0.8316 (mtm) cc_final: 0.8051 (mtm) REVERT: o 4 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8268 (mmmt) REVERT: o 17 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8024 (mmtm) REVERT: o 19 GLN cc_start: 0.9072 (pp30) cc_final: 0.8471 (pp30) REVERT: o 38 GLN cc_start: 0.7731 (pt0) cc_final: 0.6882 (pm20) REVERT: p 43 GLU cc_start: 0.7377 (tp30) cc_final: 0.7038 (tp30) REVERT: p 50 ARG cc_start: 0.9142 (ttt90) cc_final: 0.8805 (ttt-90) REVERT: p 52 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7438 (mmm160) REVERT: p 61 ARG cc_start: 0.8369 (ttt90) cc_final: 0.7784 (tpp80) REVERT: p 70 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7626 (mt-10) REVERT: q 4 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8057 (mtmt) REVERT: q 57 ARG cc_start: 0.8386 (ttt90) cc_final: 0.8135 (tpp80) REVERT: r 10 LYS cc_start: 0.6968 (mtmm) cc_final: 0.6288 (mtpp) REVERT: s 31 GLN cc_start: 0.7984 (tt0) cc_final: 0.7719 (tt0) REVERT: s 68 ASP cc_start: 0.9089 (t0) cc_final: 0.8443 (t0) REVERT: s 78 GLU cc_start: 0.7508 (tp30) cc_final: 0.7283 (tp30) REVERT: s 109 ASP cc_start: 0.7632 (p0) cc_final: 0.6071 (t0) REVERT: t 89 GLU cc_start: 0.9014 (mm-30) cc_final: 0.7858 (tm-30) REVERT: u 16 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7140 (tppt) REVERT: u 61 GLU cc_start: 0.5755 (mp0) cc_final: 0.5472 (mp0) REVERT: u 64 ILE cc_start: 0.7792 (tt) cc_final: 0.7572 (tt) REVERT: u 65 GLN cc_start: 0.8271 (mp10) cc_final: 0.7777 (mp10) REVERT: u 68 ASN cc_start: 0.7471 (m110) cc_final: 0.5575 (m110) REVERT: u 76 THR cc_start: 0.6113 (p) cc_final: 0.5858 (p) REVERT: v 46 LYS cc_start: 0.9646 (mtpt) cc_final: 0.9297 (mtmm) REVERT: v 68 LYS cc_start: 0.9367 (mmpt) cc_final: 0.9159 (mmmt) REVERT: v 76 ASP cc_start: 0.8131 (m-30) cc_final: 0.7856 (m-30) REVERT: w 21 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8068 (mmm-85) REVERT: w 60 ASP cc_start: 0.8732 (t0) cc_final: 0.8513 (t0) REVERT: x 63 ILE cc_start: 0.7538 (tp) cc_final: 0.7334 (tp) REVERT: y 26 PHE cc_start: 0.8374 (t80) cc_final: 0.8063 (t80) REVERT: z 57 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6088 (tm-30) REVERT: F 2 LYS cc_start: 0.7197 (mmmt) cc_final: 0.6842 (mtpt) REVERT: F 34 LYS cc_start: 0.8133 (mttt) cc_final: 0.7797 (mtpt) REVERT: F 35 GLN cc_start: 0.7047 (pt0) cc_final: 0.6470 (pm20) REVERT: G 7 ASP cc_start: 0.9263 (t0) cc_final: 0.9004 (t0) REVERT: G 8 MET cc_start: 0.8185 (mpp) cc_final: 0.7862 (mpp) REVERT: G 18 GLN cc_start: 0.7057 (pm20) cc_final: 0.6795 (pm20) REVERT: G 21 TYR cc_start: 0.7026 (m-80) cc_final: 0.6378 (m-80) REVERT: G 22 TRP cc_start: 0.6582 (p-90) cc_final: 0.6083 (p-90) REVERT: G 68 PHE cc_start: 0.7303 (m-80) cc_final: 0.7039 (m-80) REVERT: G 89 PHE cc_start: 0.6816 (m-10) cc_final: 0.6368 (m-10) REVERT: G 92 ASN cc_start: 0.9141 (p0) cc_final: 0.8909 (p0) REVERT: G 117 GLU cc_start: 0.5391 (mp0) cc_final: 0.4900 (mp0) REVERT: G 121 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8928 (mm-40) REVERT: G 136 ARG cc_start: 0.7082 (ttt90) cc_final: 0.6815 (ttt90) REVERT: G 153 MET cc_start: 0.7235 (mmp) cc_final: 0.6482 (mmp) REVERT: G 212 TYR cc_start: 0.8842 (m-10) cc_final: 0.8399 (m-80) REVERT: H 69 THR cc_start: 0.7278 (p) cc_final: 0.6891 (t) REVERT: H 81 GLU cc_start: 0.9184 (mp0) cc_final: 0.8963 (mp0) REVERT: H 86 LEU cc_start: 0.8978 (tt) cc_final: 0.8758 (tt) REVERT: H 168 ARG cc_start: 0.6896 (ppt170) cc_final: 0.6575 (ptt180) REVERT: H 169 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7082 (tm-30) REVERT: I 13 ARG cc_start: 0.5106 (tpp-160) cc_final: 0.4488 (tpt170) REVERT: I 47 LEU cc_start: 0.6773 (mt) cc_final: 0.6569 (mt) REVERT: I 50 TYR cc_start: 0.7350 (t80) cc_final: 0.6940 (t80) REVERT: I 53 GLN cc_start: 0.7704 (pt0) cc_final: 0.7437 (pt0) REVERT: I 62 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7258 (mmt180) REVERT: I 64 TYR cc_start: 0.6441 (m-80) cc_final: 0.6141 (m-10) REVERT: I 76 LYS cc_start: 0.6009 (mptt) cc_final: 0.5534 (mptt) REVERT: I 104 MET cc_start: 0.3281 (mmp) cc_final: 0.3035 (mmm) REVERT: J 70 MET cc_start: 0.7408 (mtp) cc_final: 0.6546 (mtt) REVERT: J 127 TYR cc_start: 0.6654 (m-80) cc_final: 0.6294 (m-80) REVERT: J 150 GLU cc_start: 0.8986 (pm20) cc_final: 0.8668 (pm20) REVERT: K 40 GLU cc_start: 0.8103 (tt0) cc_final: 0.7136 (tp30) REVERT: K 90 MET cc_start: 0.7879 (mmp) cc_final: 0.7642 (mmp) REVERT: L 47 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8555 (tm-30) REVERT: L 49 LEU cc_start: 0.8814 (mm) cc_final: 0.8415 (pp) REVERT: L 121 ASN cc_start: 0.8455 (m-40) cc_final: 0.8139 (m110) REVERT: M 2 MET cc_start: 0.6710 (tpt) cc_final: 0.5985 (tpt) REVERT: M 9 MET cc_start: 0.6653 (ttp) cc_final: 0.5549 (tmm) REVERT: M 26 MET cc_start: 0.7497 (ptp) cc_final: 0.6693 (ptp) REVERT: M 57 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7278 (mp0) REVERT: M 72 GLU cc_start: 0.7760 (mp0) cc_final: 0.7382 (mp0) REVERT: M 87 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6053 (tpp-160) REVERT: N 24 ASN cc_start: 0.9134 (t0) cc_final: 0.8592 (t0) REVERT: N 45 MET cc_start: 0.8926 (mmp) cc_final: 0.8684 (mmm) REVERT: N 67 LYS cc_start: 0.7838 (ptpp) cc_final: 0.7070 (tptp) REVERT: O 15 HIS cc_start: 0.7336 (p-80) cc_final: 0.6754 (p-80) REVERT: O 66 GLU cc_start: 0.8220 (pp20) cc_final: 0.7347 (tm-30) REVERT: O 67 ILE cc_start: 0.8247 (tt) cc_final: 0.7536 (tt) REVERT: O 88 MET cc_start: 0.5195 (mmt) cc_final: 0.4146 (ppp) REVERT: P 118 ASN cc_start: 0.8384 (t0) cc_final: 0.6584 (p0) REVERT: Q 14 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8460 (tptp) REVERT: Q 76 HIS cc_start: 0.8329 (m-70) cc_final: 0.8019 (m-70) REVERT: R 2 ARG cc_start: 0.5972 (tpt170) cc_final: 0.5697 (tpt-90) REVERT: R 22 TYR cc_start: 0.7608 (t80) cc_final: 0.7361 (t80) REVERT: R 70 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8937 (mtp180) REVERT: R 74 MET cc_start: 0.8066 (ppp) cc_final: 0.7857 (ppp) REVERT: S 15 LEU cc_start: 0.8483 (tp) cc_final: 0.8144 (tp) REVERT: S 61 ASN cc_start: 0.8635 (t0) cc_final: 0.8416 (t0) REVERT: T 46 LYS cc_start: 0.6978 (mtmm) cc_final: 0.6690 (mmmt) REVERT: U 31 ARG cc_start: 0.8188 (mmt180) cc_final: 0.7604 (mmt90) REVERT: U 79 ASN cc_start: 0.8384 (p0) cc_final: 0.8108 (p0) REVERT: V 45 VAL cc_start: 0.7916 (t) cc_final: 0.7715 (t) REVERT: V 62 GLU cc_start: 0.6813 (tp30) cc_final: 0.6387 (tp30) REVERT: W 51 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8128 (tp-100) REVERT: X 65 MET cc_start: 0.7557 (ptt) cc_final: 0.7202 (ptt) REVERT: Y 15 LYS cc_start: 0.9071 (pptt) cc_final: 0.8784 (pptt) REVERT: Y 30 PHE cc_start: 0.9002 (m-80) cc_final: 0.8419 (m-80) REVERT: Y 39 GLU cc_start: 0.8801 (mp0) cc_final: 0.8480 (mp0) REVERT: Y 42 ASP cc_start: 0.8528 (t0) cc_final: 0.8100 (t0) REVERT: Y 78 LEU cc_start: 0.8986 (mm) cc_final: 0.8744 (mm) REVERT: a 7 ARG cc_start: 0.6877 (tpt90) cc_final: 0.6048 (mtt180) REVERT: a 167 LYS cc_start: 0.9115 (mttt) cc_final: 0.8817 (mttt) outliers start: 4 outliers final: 1 residues processed: 1490 average time/residue: 1.4703 time to fit residues: 3730.6276 Evaluate side-chains 1247 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1246 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 10.0000 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 40.0000 chunk 975 optimal weight: 10.9990 chunk 571 optimal weight: 50.0000 chunk 413 optimal weight: 8.9990 chunk 745 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 857 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 overall best weight: 7.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 259 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 ASN v 5 ASN ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 163139 Z= 0.374 Angle : 0.846 15.465 244082 Z= 0.424 Chirality : 0.045 0.305 31220 Planarity : 0.007 0.096 13080 Dihedral : 24.319 178.580 81722 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 33.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.89 % Favored : 86.01 % Rotamer: Outliers : 0.06 % Allowed : 1.32 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5919 helix: -1.57 (0.11), residues: 1785 sheet: -2.22 (0.16), residues: 874 loop : -2.69 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP b 212 HIS 0.012 0.002 HIS o 100 PHE 0.032 0.003 PHE g 46 TYR 0.031 0.003 TYR K 49 ARG 0.014 0.001 ARG b 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1406 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 81 GLU cc_start: 0.7979 (tp30) cc_final: 0.7717 (tp30) REVERT: b 82 TYR cc_start: 0.7551 (t80) cc_final: 0.6898 (t80) REVERT: b 99 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7590 (mm-30) REVERT: b 196 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8250 (t0) REVERT: b 200 MET cc_start: 0.8235 (ptt) cc_final: 0.7885 (tmm) REVERT: c 1 MET cc_start: 0.8488 (mtm) cc_final: 0.8232 (mtm) REVERT: c 26 VAL cc_start: 0.8819 (t) cc_final: 0.8498 (m) REVERT: c 28 GLU cc_start: 0.6924 (tm-30) cc_final: 0.5811 (tm-30) REVERT: d 51 GLU cc_start: 0.8122 (tt0) cc_final: 0.7727 (tt0) REVERT: d 74 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8135 (mmmm) REVERT: d 133 LEU cc_start: 0.9306 (tp) cc_final: 0.9006 (tp) REVERT: d 136 GLN cc_start: 0.7894 (pp30) cc_final: 0.7663 (pp30) REVERT: d 157 LEU cc_start: 0.8879 (mt) cc_final: 0.8463 (mt) REVERT: d 183 PHE cc_start: 0.6264 (m-80) cc_final: 0.5383 (m-80) REVERT: d 184 ASP cc_start: 0.7709 (m-30) cc_final: 0.7113 (m-30) REVERT: d 188 MET cc_start: 0.5376 (ptp) cc_final: 0.4898 (ptm) REVERT: d 194 LYS cc_start: 0.9443 (mmpt) cc_final: 0.9234 (mmmt) REVERT: e 19 PHE cc_start: 0.8343 (m-80) cc_final: 0.8055 (m-80) REVERT: e 21 TYR cc_start: 0.8445 (m-10) cc_final: 0.7653 (m-10) REVERT: e 25 MET cc_start: 0.8166 (mpp) cc_final: 0.7407 (mpp) REVERT: e 29 ARG cc_start: 0.7562 (mpp-170) cc_final: 0.7078 (tpt-90) REVERT: e 56 LEU cc_start: 0.9050 (tp) cc_final: 0.8800 (tt) REVERT: e 82 TYR cc_start: 0.7919 (t80) cc_final: 0.7314 (t80) REVERT: e 90 LEU cc_start: 0.9159 (tp) cc_final: 0.8949 (tp) REVERT: f 41 GLU cc_start: 0.8953 (tt0) cc_final: 0.8140 (tm-30) REVERT: f 54 ARG cc_start: 0.8517 (ttm110) cc_final: 0.7992 (ttm110) REVERT: f 127 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7468 (mm-40) REVERT: f 133 LYS cc_start: 0.7207 (tptt) cc_final: 0.6877 (tppt) REVERT: g 7 ASP cc_start: 0.7717 (p0) cc_final: 0.7446 (p0) REVERT: g 8 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8677 (tptp) REVERT: h 1 MET cc_start: 0.5961 (ppp) cc_final: 0.5720 (ppp) REVERT: i 124 MET cc_start: -0.3990 (ptp) cc_final: -0.4416 (mmm) REVERT: i 135 MET cc_start: 0.5683 (ptp) cc_final: 0.5238 (mmt) REVERT: j 31 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7544 (mm-30) REVERT: j 41 LYS cc_start: 0.8850 (mttt) cc_final: 0.8616 (mttt) REVERT: j 67 ASN cc_start: 0.7427 (t0) cc_final: 0.7063 (t0) REVERT: j 71 ASP cc_start: 0.8654 (m-30) cc_final: 0.7932 (m-30) REVERT: j 95 ARG cc_start: 0.7841 (mpt180) cc_final: 0.7555 (mmt180) REVERT: j 118 MET cc_start: 0.8899 (ptp) cc_final: 0.8682 (ptp) REVERT: k 2 ILE cc_start: 0.7819 (mm) cc_final: 0.7265 (mm) REVERT: k 22 ILE cc_start: 0.8263 (pt) cc_final: 0.8046 (pt) REVERT: k 29 HIS cc_start: 0.8280 (t70) cc_final: 0.7904 (t70) REVERT: k 79 PHE cc_start: 0.7735 (m-80) cc_final: 0.7183 (m-80) REVERT: k 98 ARG cc_start: 0.8343 (ttm110) cc_final: 0.7988 (ttm110) REVERT: l 55 MET cc_start: 0.8435 (mmp) cc_final: 0.7932 (mmp) REVERT: l 59 ARG cc_start: 0.8509 (mtp85) cc_final: 0.7703 (mtp85) REVERT: m 81 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6657 (mtt180) REVERT: m 106 ASP cc_start: 0.9107 (p0) cc_final: 0.8789 (p0) REVERT: m 111 GLU cc_start: 0.8684 (tp30) cc_final: 0.8433 (tp30) REVERT: n 24 MET cc_start: 0.7682 (mtp) cc_final: 0.7289 (mtt) REVERT: n 29 VAL cc_start: 0.8911 (t) cc_final: 0.8668 (p) REVERT: n 32 GLU cc_start: 0.8417 (mp0) cc_final: 0.8045 (mp0) REVERT: n 62 ASN cc_start: 0.8357 (m-40) cc_final: 0.8124 (m-40) REVERT: n 73 ASN cc_start: 0.8722 (m-40) cc_final: 0.8474 (m-40) REVERT: o 4 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8484 (mmmt) REVERT: o 38 GLN cc_start: 0.7838 (pt0) cc_final: 0.6910 (pm20) REVERT: o 98 GLN cc_start: 0.6448 (tp-100) cc_final: 0.6115 (mm110) REVERT: p 10 GLU cc_start: 0.7712 (mp0) cc_final: 0.7084 (mp0) REVERT: p 43 GLU cc_start: 0.7319 (tp30) cc_final: 0.7038 (tp30) REVERT: p 52 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7513 (mmm160) REVERT: p 70 GLU cc_start: 0.8764 (mt-10) cc_final: 0.7830 (mt-10) REVERT: p 105 LYS cc_start: 0.8887 (tptp) cc_final: 0.8645 (tptp) REVERT: q 4 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8145 (mtmt) REVERT: q 16 ILE cc_start: 0.8030 (mt) cc_final: 0.7771 (mt) REVERT: q 83 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8229 (ttmm) REVERT: s 31 GLN cc_start: 0.8041 (tt0) cc_final: 0.7745 (tt0) REVERT: s 68 ASP cc_start: 0.9139 (t0) cc_final: 0.8553 (t70) REVERT: s 109 ASP cc_start: 0.7510 (p0) cc_final: 0.5811 (t0) REVERT: t 89 GLU cc_start: 0.9030 (mm-30) cc_final: 0.7851 (tm-30) REVERT: u 39 ASN cc_start: 0.8655 (m-40) cc_final: 0.8161 (m110) REVERT: u 64 ILE cc_start: 0.7784 (tt) cc_final: 0.7514 (tt) REVERT: u 65 GLN cc_start: 0.8292 (mp10) cc_final: 0.7798 (mp10) REVERT: u 68 ASN cc_start: 0.7609 (m110) cc_final: 0.6047 (m110) REVERT: v 46 LYS cc_start: 0.9669 (mtpt) cc_final: 0.9335 (mtmm) REVERT: v 68 LYS cc_start: 0.9390 (mmpt) cc_final: 0.9178 (mmmt) REVERT: v 76 ASP cc_start: 0.8136 (m-30) cc_final: 0.7868 (m-30) REVERT: w 21 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.8180 (mmm-85) REVERT: w 60 ASP cc_start: 0.8819 (t0) cc_final: 0.8598 (t0) REVERT: x 15 ASN cc_start: 0.8361 (m110) cc_final: 0.8159 (m110) REVERT: y 26 PHE cc_start: 0.8347 (t80) cc_final: 0.8062 (t80) REVERT: z 55 LYS cc_start: 0.8546 (tmtt) cc_final: 0.8303 (tptt) REVERT: z 57 GLU cc_start: 0.6468 (tm-30) cc_final: 0.6151 (tm-30) REVERT: F 2 LYS cc_start: 0.7466 (mmmt) cc_final: 0.7074 (mtpt) REVERT: F 34 LYS cc_start: 0.8265 (mttt) cc_final: 0.7797 (mtpt) REVERT: F 35 GLN cc_start: 0.7273 (pt0) cc_final: 0.6548 (pm20) REVERT: G 8 MET cc_start: 0.8284 (mpp) cc_final: 0.8037 (mpp) REVERT: G 18 GLN cc_start: 0.7094 (pm20) cc_final: 0.6712 (pm20) REVERT: G 21 TYR cc_start: 0.7310 (m-80) cc_final: 0.6516 (m-80) REVERT: G 22 TRP cc_start: 0.6553 (p-90) cc_final: 0.6057 (p-90) REVERT: G 25 LYS cc_start: 0.8101 (tppt) cc_final: 0.7812 (tmtt) REVERT: G 68 PHE cc_start: 0.7254 (m-80) cc_final: 0.7050 (m-80) REVERT: G 89 PHE cc_start: 0.6100 (m-10) cc_final: 0.5604 (m-10) REVERT: G 92 ASN cc_start: 0.9153 (p0) cc_final: 0.8927 (p0) REVERT: G 117 GLU cc_start: 0.6020 (mp0) cc_final: 0.5191 (mp0) REVERT: G 121 GLN cc_start: 0.9334 (mm-40) cc_final: 0.8974 (mm-40) REVERT: G 153 MET cc_start: 0.7730 (mmp) cc_final: 0.7080 (mmp) REVERT: G 212 TYR cc_start: 0.8884 (m-10) cc_final: 0.8381 (m-80) REVERT: H 69 THR cc_start: 0.7280 (p) cc_final: 0.6917 (t) REVERT: H 151 GLU cc_start: 0.7843 (mp0) cc_final: 0.6893 (mp0) REVERT: H 160 GLU cc_start: 0.7277 (pt0) cc_final: 0.6997 (pt0) REVERT: H 169 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7762 (tm-30) REVERT: I 47 LEU cc_start: 0.6851 (mt) cc_final: 0.6639 (mt) REVERT: I 50 TYR cc_start: 0.7491 (t80) cc_final: 0.6924 (t80) REVERT: I 62 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7321 (mmt180) REVERT: I 64 TYR cc_start: 0.5987 (m-80) cc_final: 0.5645 (m-10) REVERT: I 76 LYS cc_start: 0.5908 (mptt) cc_final: 0.5030 (mptt) REVERT: I 104 MET cc_start: 0.3291 (mmp) cc_final: 0.2954 (mmm) REVERT: J 70 MET cc_start: 0.7399 (mtp) cc_final: 0.6653 (mtt) REVERT: J 127 TYR cc_start: 0.6945 (m-80) cc_final: 0.6622 (m-80) REVERT: J 131 ASN cc_start: 0.8696 (t0) cc_final: 0.8478 (t0) REVERT: J 150 GLU cc_start: 0.8905 (pm20) cc_final: 0.8676 (pm20) REVERT: J 151 MET cc_start: 0.8456 (mmp) cc_final: 0.8223 (mmm) REVERT: K 40 GLU cc_start: 0.8154 (tt0) cc_final: 0.7054 (tp30) REVERT: K 41 ASP cc_start: 0.7722 (t0) cc_final: 0.7516 (t0) REVERT: K 73 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7603 (mt-10) REVERT: L 47 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8525 (tm-30) REVERT: L 48 THR cc_start: 0.8663 (p) cc_final: 0.8196 (p) REVERT: L 49 LEU cc_start: 0.8969 (mm) cc_final: 0.8540 (pp) REVERT: L 51 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8555 (mm-40) REVERT: L 115 MET cc_start: 0.6283 (tpp) cc_final: 0.5958 (tpp) REVERT: L 121 ASN cc_start: 0.8495 (m-40) cc_final: 0.8191 (m110) REVERT: L 125 ASP cc_start: 0.8690 (m-30) cc_final: 0.8448 (m-30) REVERT: M 2 MET cc_start: 0.6599 (tpt) cc_final: 0.5857 (tpt) REVERT: M 9 MET cc_start: 0.6562 (ttp) cc_final: 0.5520 (tmm) REVERT: M 26 MET cc_start: 0.7389 (ptp) cc_final: 0.6476 (ptp) REVERT: M 57 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7197 (mp0) REVERT: M 95 MET cc_start: 0.7301 (tpp) cc_final: 0.6919 (tpp) REVERT: N 24 ASN cc_start: 0.9232 (t0) cc_final: 0.8713 (t0) REVERT: N 33 SER cc_start: 0.8220 (t) cc_final: 0.7984 (p) REVERT: O 15 HIS cc_start: 0.7320 (p-80) cc_final: 0.6754 (p-80) REVERT: O 66 GLU cc_start: 0.8286 (pp20) cc_final: 0.7655 (tm-30) REVERT: O 88 MET cc_start: 0.5210 (mmt) cc_final: 0.4247 (ppp) REVERT: P 118 ASN cc_start: 0.8358 (t0) cc_final: 0.6605 (p0) REVERT: Q 76 HIS cc_start: 0.8370 (m-70) cc_final: 0.8039 (m-70) REVERT: R 2 ARG cc_start: 0.6048 (tpt170) cc_final: 0.5791 (tpt-90) REVERT: R 22 TYR cc_start: 0.7602 (t80) cc_final: 0.7151 (t80) REVERT: R 70 ARG cc_start: 0.9122 (mtt180) cc_final: 0.8913 (mtp180) REVERT: R 74 MET cc_start: 0.8223 (ppp) cc_final: 0.7936 (ppp) REVERT: S 15 LEU cc_start: 0.8397 (tp) cc_final: 0.8093 (tp) REVERT: S 61 ASN cc_start: 0.8633 (t0) cc_final: 0.8407 (t0) REVERT: T 10 ILE cc_start: 0.9050 (mp) cc_final: 0.8573 (mp) REVERT: T 14 PHE cc_start: 0.8343 (m-10) cc_final: 0.8138 (m-80) REVERT: T 46 LYS cc_start: 0.6978 (mtmm) cc_final: 0.6654 (mmmt) REVERT: U 79 ASN cc_start: 0.8407 (p0) cc_final: 0.8121 (p0) REVERT: V 62 GLU cc_start: 0.6800 (tp30) cc_final: 0.6491 (tp30) REVERT: W 51 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8343 (tp-100) REVERT: X 35 ARG cc_start: 0.3509 (ttt180) cc_final: 0.3283 (ttt180) REVERT: X 65 MET cc_start: 0.7594 (ptt) cc_final: 0.7142 (ptt) REVERT: Y 15 LYS cc_start: 0.9080 (pptt) cc_final: 0.8793 (pptt) REVERT: Y 30 PHE cc_start: 0.8987 (m-80) cc_final: 0.8337 (m-80) REVERT: Y 42 ASP cc_start: 0.8565 (t0) cc_final: 0.8129 (t0) REVERT: Y 78 LEU cc_start: 0.8979 (mm) cc_final: 0.8725 (mm) REVERT: a 7 ARG cc_start: 0.6839 (tpt90) cc_final: 0.5880 (mtt180) REVERT: a 8 MET cc_start: 0.6894 (mpp) cc_final: 0.6446 (mpp) REVERT: a 167 LYS cc_start: 0.9113 (mttt) cc_final: 0.8837 (mttt) outliers start: 3 outliers final: 0 residues processed: 1408 average time/residue: 1.4012 time to fit residues: 3353.8761 Evaluate side-chains 1220 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1219 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 50.0000 chunk 623 optimal weight: 30.0000 chunk 1003 optimal weight: 10.0000 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 6.9990 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 20.0000 chunk 969 optimal weight: 10.0000 chunk 838 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 647 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 55 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN ** v 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 163139 Z= 0.429 Angle : 0.917 16.900 244082 Z= 0.458 Chirality : 0.048 0.375 31220 Planarity : 0.007 0.128 13080 Dihedral : 24.559 178.936 81722 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 36.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.73 % Favored : 85.13 % Rotamer: Outliers : 0.06 % Allowed : 0.92 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.10), residues: 5919 helix: -1.77 (0.11), residues: 1781 sheet: -2.31 (0.17), residues: 843 loop : -2.79 (0.10), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.003 TRP b 212 HIS 0.014 0.002 HIS v 88 PHE 0.032 0.003 PHE g 46 TYR 0.042 0.003 TYR j 44 ARG 0.019 0.001 ARG V 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1383 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 32 LEU cc_start: 0.9086 (mt) cc_final: 0.8369 (mt) REVERT: b 81 GLU cc_start: 0.7953 (tp30) cc_final: 0.7736 (tp30) REVERT: b 99 GLU cc_start: 0.7953 (mm-30) cc_final: 0.6622 (mt-10) REVERT: b 131 MET cc_start: 0.8985 (mpp) cc_final: 0.8710 (mpp) REVERT: b 200 MET cc_start: 0.8274 (ptt) cc_final: 0.7968 (tmm) REVERT: b 212 TRP cc_start: 0.8166 (p90) cc_final: 0.7954 (p90) REVERT: b 252 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8114 (ttmt) REVERT: d 25 GLU cc_start: 0.7186 (tt0) cc_final: 0.6759 (tt0) REVERT: d 51 GLU cc_start: 0.8069 (tt0) cc_final: 0.7681 (tt0) REVERT: d 74 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8220 (mmmm) REVERT: d 133 LEU cc_start: 0.9370 (tp) cc_final: 0.9062 (tp) REVERT: d 136 GLN cc_start: 0.7977 (pp30) cc_final: 0.7742 (pp30) REVERT: d 158 PHE cc_start: 0.8787 (t80) cc_final: 0.8558 (t80) REVERT: d 188 MET cc_start: 0.5490 (ptp) cc_final: 0.5018 (ptm) REVERT: d 194 LYS cc_start: 0.9494 (mmpt) cc_final: 0.9264 (mmmt) REVERT: e 19 PHE cc_start: 0.8463 (m-80) cc_final: 0.8182 (m-80) REVERT: e 21 TYR cc_start: 0.8451 (m-10) cc_final: 0.7641 (m-10) REVERT: e 25 MET cc_start: 0.8198 (mpp) cc_final: 0.7874 (mpp) REVERT: e 56 LEU cc_start: 0.8986 (tp) cc_final: 0.8756 (tt) REVERT: e 82 TYR cc_start: 0.7975 (t80) cc_final: 0.7390 (t80) REVERT: e 90 LEU cc_start: 0.9213 (tp) cc_final: 0.8921 (tp) REVERT: f 41 GLU cc_start: 0.8975 (tt0) cc_final: 0.8155 (tm-30) REVERT: f 54 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8055 (ttm110) REVERT: f 133 LYS cc_start: 0.7201 (tptt) cc_final: 0.6890 (tppt) REVERT: f 142 GLN cc_start: 0.7477 (mm110) cc_final: 0.6871 (mm-40) REVERT: i 124 MET cc_start: -0.3853 (ptp) cc_final: -0.4178 (mmp) REVERT: i 135 MET cc_start: 0.5938 (ptp) cc_final: 0.5363 (mmt) REVERT: j 10 THR cc_start: 0.9196 (p) cc_final: 0.8970 (p) REVERT: j 31 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7565 (mm-30) REVERT: j 67 ASN cc_start: 0.7445 (t0) cc_final: 0.7113 (t0) REVERT: j 71 ASP cc_start: 0.8693 (m-30) cc_final: 0.8143 (m-30) REVERT: j 95 ARG cc_start: 0.7923 (mpt180) cc_final: 0.7605 (mmt180) REVERT: j 118 MET cc_start: 0.8873 (ptp) cc_final: 0.8550 (ptp) REVERT: k 22 ILE cc_start: 0.8359 (pt) cc_final: 0.8156 (pt) REVERT: k 29 HIS cc_start: 0.8395 (t70) cc_final: 0.7931 (t70) REVERT: k 98 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7902 (ttm110) REVERT: l 55 MET cc_start: 0.8454 (mmp) cc_final: 0.7910 (mmp) REVERT: l 59 ARG cc_start: 0.8570 (mtp85) cc_final: 0.7624 (mtp85) REVERT: m 81 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6676 (mtt180) REVERT: m 106 ASP cc_start: 0.9120 (p0) cc_final: 0.8820 (p0) REVERT: m 111 GLU cc_start: 0.8631 (tp30) cc_final: 0.8272 (tp30) REVERT: n 4 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7043 (mmm160) REVERT: n 24 MET cc_start: 0.7664 (mtp) cc_final: 0.7208 (mtt) REVERT: n 32 GLU cc_start: 0.8417 (mp0) cc_final: 0.8155 (mp0) REVERT: n 62 ASN cc_start: 0.8386 (m-40) cc_final: 0.8148 (m110) REVERT: n 73 ASN cc_start: 0.8693 (m-40) cc_final: 0.8425 (m-40) REVERT: o 4 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8472 (mmmt) REVERT: o 38 GLN cc_start: 0.7905 (pt0) cc_final: 0.6949 (pm20) REVERT: p 10 GLU cc_start: 0.7914 (mp0) cc_final: 0.7289 (mp0) REVERT: p 43 GLU cc_start: 0.7379 (tp30) cc_final: 0.7076 (tp30) REVERT: p 52 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7442 (mmm160) REVERT: p 70 GLU cc_start: 0.8708 (mt-10) cc_final: 0.7442 (mt-10) REVERT: q 4 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8191 (mtmt) REVERT: q 16 ILE cc_start: 0.8142 (mt) cc_final: 0.7889 (mt) REVERT: q 93 ILE cc_start: 0.8685 (mm) cc_final: 0.8403 (mm) REVERT: s 31 GLN cc_start: 0.8114 (tt0) cc_final: 0.7799 (tt0) REVERT: s 68 ASP cc_start: 0.9087 (t0) cc_final: 0.8495 (t0) REVERT: s 109 ASP cc_start: 0.7599 (p0) cc_final: 0.6002 (t0) REVERT: t 89 GLU cc_start: 0.9011 (mm-30) cc_final: 0.7850 (tm-30) REVERT: u 39 ASN cc_start: 0.8331 (m-40) cc_final: 0.7748 (m110) REVERT: u 61 GLU cc_start: 0.6018 (mp0) cc_final: 0.5668 (mp0) REVERT: u 64 ILE cc_start: 0.7696 (tt) cc_final: 0.7388 (tt) REVERT: u 65 GLN cc_start: 0.8305 (mp10) cc_final: 0.7776 (mp10) REVERT: u 68 ASN cc_start: 0.7574 (m110) cc_final: 0.6014 (m110) REVERT: v 76 ASP cc_start: 0.8156 (m-30) cc_final: 0.7863 (m-30) REVERT: w 25 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6899 (mt-10) REVERT: w 58 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7817 (mtpp) REVERT: w 60 ASP cc_start: 0.8787 (t0) cc_final: 0.8568 (t0) REVERT: x 63 ILE cc_start: 0.7405 (tp) cc_final: 0.7175 (pt) REVERT: y 26 PHE cc_start: 0.8404 (t80) cc_final: 0.8075 (t80) REVERT: z 55 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8194 (tptt) REVERT: z 57 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6358 (tm-30) REVERT: F 34 LYS cc_start: 0.8226 (mttt) cc_final: 0.7953 (mtpt) REVERT: G 8 MET cc_start: 0.8313 (mpp) cc_final: 0.8101 (mpp) REVERT: G 21 TYR cc_start: 0.7458 (m-80) cc_final: 0.6856 (m-80) REVERT: G 22 TRP cc_start: 0.6587 (p-90) cc_final: 0.6100 (p-90) REVERT: G 26 MET cc_start: 0.6795 (mmm) cc_final: 0.5290 (mmm) REVERT: G 77 GLU cc_start: 0.8228 (pm20) cc_final: 0.7850 (pm20) REVERT: G 89 PHE cc_start: 0.5898 (m-10) cc_final: 0.5623 (m-10) REVERT: G 92 ASN cc_start: 0.9214 (p0) cc_final: 0.8932 (p0) REVERT: G 117 GLU cc_start: 0.5270 (mp0) cc_final: 0.4475 (mp0) REVERT: G 121 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8960 (mm-40) REVERT: G 174 GLU cc_start: 0.7035 (mt-10) cc_final: 0.5740 (mp0) REVERT: G 211 LEU cc_start: 0.8644 (pp) cc_final: 0.8433 (pp) REVERT: G 212 TYR cc_start: 0.8827 (m-10) cc_final: 0.8151 (m-80) REVERT: H 54 ILE cc_start: 0.9380 (tt) cc_final: 0.8802 (tt) REVERT: H 84 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8575 (mp0) REVERT: H 86 LEU cc_start: 0.9214 (tt) cc_final: 0.8956 (tt) REVERT: H 151 GLU cc_start: 0.7838 (mp0) cc_final: 0.7002 (mp0) REVERT: H 160 GLU cc_start: 0.7456 (pt0) cc_final: 0.7192 (pt0) REVERT: H 169 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7194 (tm-30) REVERT: I 47 LEU cc_start: 0.6675 (mt) cc_final: 0.6417 (mt) REVERT: I 50 TYR cc_start: 0.7395 (t80) cc_final: 0.6722 (t80) REVERT: I 62 ARG cc_start: 0.7419 (mmt180) cc_final: 0.7215 (mmt180) REVERT: I 64 TYR cc_start: 0.5932 (m-80) cc_final: 0.5617 (m-80) REVERT: I 76 LYS cc_start: 0.5943 (mptt) cc_final: 0.5083 (mptt) REVERT: I 104 MET cc_start: 0.3664 (mmp) cc_final: 0.3321 (mmm) REVERT: I 114 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7528 (ptt-90) REVERT: J 67 ARG cc_start: 0.8850 (ptp90) cc_final: 0.8546 (mtm110) REVERT: J 131 ASN cc_start: 0.8646 (t0) cc_final: 0.8413 (t0) REVERT: J 150 GLU cc_start: 0.8849 (pm20) cc_final: 0.8642 (pm20) REVERT: J 151 MET cc_start: 0.8575 (mmp) cc_final: 0.8212 (mmm) REVERT: K 40 GLU cc_start: 0.8388 (tt0) cc_final: 0.7422 (pm20) REVERT: K 90 MET cc_start: 0.8287 (mmp) cc_final: 0.7913 (mmp) REVERT: L 47 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8481 (tm-30) REVERT: L 48 THR cc_start: 0.8774 (p) cc_final: 0.8326 (p) REVERT: L 51 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8542 (mm-40) REVERT: L 115 MET cc_start: 0.6322 (tpp) cc_final: 0.5957 (tpp) REVERT: L 121 ASN cc_start: 0.8468 (m-40) cc_final: 0.8196 (m110) REVERT: L 125 ASP cc_start: 0.8550 (m-30) cc_final: 0.8241 (m-30) REVERT: M 2 MET cc_start: 0.6652 (tpt) cc_final: 0.6025 (tpt) REVERT: M 8 ASP cc_start: 0.8595 (m-30) cc_final: 0.8204 (m-30) REVERT: M 9 MET cc_start: 0.6518 (ttp) cc_final: 0.5471 (tmm) REVERT: M 26 MET cc_start: 0.7385 (ptp) cc_final: 0.6506 (ptp) REVERT: M 57 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7226 (mp0) REVERT: M 62 LEU cc_start: 0.8280 (mt) cc_final: 0.7641 (mt) REVERT: M 95 MET cc_start: 0.7398 (tpp) cc_final: 0.7010 (tpp) REVERT: N 24 ASN cc_start: 0.9255 (t0) cc_final: 0.8762 (t0) REVERT: N 26 LYS cc_start: 0.7918 (tttm) cc_final: 0.7607 (tttp) REVERT: O 15 HIS cc_start: 0.7221 (p-80) cc_final: 0.6843 (p-80) REVERT: O 66 GLU cc_start: 0.8219 (pp20) cc_final: 0.7561 (pp20) REVERT: O 67 ILE cc_start: 0.7707 (tt) cc_final: 0.7359 (tt) REVERT: P 41 LEU cc_start: 0.9179 (mt) cc_final: 0.8978 (mt) REVERT: Q 76 HIS cc_start: 0.8297 (m-70) cc_final: 0.8028 (m-70) REVERT: Q 81 ILE cc_start: 0.7296 (tp) cc_final: 0.7054 (tp) REVERT: R 2 ARG cc_start: 0.6230 (tpt170) cc_final: 0.5953 (tpt-90) REVERT: R 22 TYR cc_start: 0.7584 (t80) cc_final: 0.7215 (t80) REVERT: R 74 MET cc_start: 0.8193 (ppp) cc_final: 0.7852 (ppp) REVERT: S 15 LEU cc_start: 0.8288 (tp) cc_final: 0.7998 (tp) REVERT: S 61 ASN cc_start: 0.8683 (t0) cc_final: 0.8465 (t0) REVERT: T 14 PHE cc_start: 0.8010 (m-10) cc_final: 0.7583 (m-80) REVERT: T 46 LYS cc_start: 0.7036 (mtmm) cc_final: 0.6772 (mmmt) REVERT: U 9 HIS cc_start: 0.5828 (m-70) cc_final: 0.5564 (m-70) REVERT: U 79 ASN cc_start: 0.8471 (p0) cc_final: 0.8209 (p0) REVERT: V 45 VAL cc_start: 0.7892 (t) cc_final: 0.7651 (t) REVERT: V 62 GLU cc_start: 0.6871 (tp30) cc_final: 0.6506 (tp30) REVERT: W 51 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8359 (tp-100) REVERT: X 35 ARG cc_start: 0.3467 (ttt180) cc_final: 0.3239 (ttt180) REVERT: X 65 MET cc_start: 0.7640 (ptt) cc_final: 0.7071 (ptt) REVERT: Y 15 LYS cc_start: 0.9120 (pptt) cc_final: 0.8825 (pptt) REVERT: Y 30 PHE cc_start: 0.8984 (m-80) cc_final: 0.8448 (m-80) REVERT: Y 42 ASP cc_start: 0.8712 (t0) cc_final: 0.8378 (t0) REVERT: Y 78 LEU cc_start: 0.8966 (mm) cc_final: 0.8733 (mm) REVERT: a 167 LYS cc_start: 0.9143 (mttt) cc_final: 0.8856 (mmtt) outliers start: 3 outliers final: 0 residues processed: 1384 average time/residue: 1.3968 time to fit residues: 3273.0398 Evaluate side-chains 1209 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1209 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 839 optimal weight: 50.0000 chunk 351 optimal weight: 7.9990 chunk 862 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 38 GLN q 55 GLN ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 78 GLN ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN L 67 ASN L 147 ASN M 117 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.131822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107868 restraints weight = 477176.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110392 restraints weight = 204699.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111158 restraints weight = 112938.973| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 163139 Z= 0.327 Angle : 0.805 15.187 244082 Z= 0.406 Chirality : 0.043 0.447 31220 Planarity : 0.006 0.089 13080 Dihedral : 24.458 179.950 81722 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.50 % Favored : 86.40 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.10), residues: 5919 helix: -1.54 (0.11), residues: 1772 sheet: -2.24 (0.17), residues: 853 loop : -2.68 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP b 212 HIS 0.018 0.002 HIS b 231 PHE 0.031 0.003 PHE g 46 TYR 0.034 0.003 TYR K 49 ARG 0.017 0.001 ARG J 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45705.69 seconds wall clock time: 798 minutes 13.25 seconds (47893.25 seconds total)