Starting phenix.real_space_refine on Tue Mar 26 12:34:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdb_21630/03_2024/6wdb_21630_updated.pdb" } resolution = 4.0 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= 0.124 sd= 0.876 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 65": "OD1" <-> "OD2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 179": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ASP 18": "OD1" <-> "OD2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ASP 7": "OD1" <-> "OD2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ASP 22": "OD1" <-> "OD2" Residue "d TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 116": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e ASP 9": "OD1" <-> "OD2" 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 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "f ASP 46": "OD1" <-> "OD2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 7": "OD1" <-> "OD2" Residue "g ASP 98": "OD1" <-> "OD2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "h TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 116": "OE1" <-> "OE2" Residue "h ASP 124": "OD1" <-> "OD2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "i GLU 140": "OE1" <-> "OE2" 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 43": "OE1" <-> "OE2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k ASP 80": "OD1" <-> "OD2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 121": "OE1" <-> "OE2" 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 GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" 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 ASP 70": "OD1" <-> "OD2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" 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 ASP 58": "OD1" <-> "OD2" 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 ASP 117": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ASP 23": "OD1" <-> "OD2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" 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 ARG 69": "NH1" <-> "NH2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 46": "OE1" <-> "OE2" Residue "r ASP 55": "OD1" <-> "OD2" 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 ASP 22": "OD1" <-> "OD2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" 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 GLU 25": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 41": "OE1" <-> "OE2" Residue "v ASP 45": "OD1" <-> "OD2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "x ASP 59": "OD1" <-> "OD2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 38": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" 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 ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T ASP 48": "OD1" <-> "OD2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "V ASP 14": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 58": "OD1" <-> "OD2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z ASP 12": "OD1" <-> "OD2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 166": "OD1" <-> "OD2" Residue "a ASP 181": "OD1" <-> "OD2" 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': 211, 'rna2p_pyr': 93, 'rna3p_pur': 1463, 'rna3p_pyr': 1136} Link IDs: {'rna2p': 304, 'rna3p': 2598} 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: 59.57, per 1000 atoms: 0.40 Number of scatterers: 150149 At special positions: 0 Unit cell: (279.93, 266.6, 243.939, 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: 62.26 Conformation dependent library (CDL) restraints added in 7.0 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: 181 helices and 67 sheets defined 37.9% alpha, 16.1% beta 1416 base pairs and 2995 stacking pairs defined. Time for finding SS restraints: 74.52 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 7.270A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.511A 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 198 through 203 removed outlier: 3.659A pdb=" N ARG b 202 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL b 203 " --> pdb=" O HIS b 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 198 through 203' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.451A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 5.428A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.630A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 3.780A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 105 removed outlier: 3.770A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.791A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.559A pdb=" N VAL d 28 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.729A pdb=" N VAL d 113 " --> pdb=" O LEU d 109 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.625A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 165 removed outlier: 4.552A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N HIS d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.559A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.549A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET d 199 " --> pdb=" O GLN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 removed outlier: 4.309A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 20 removed outlier: 4.034A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 4.590A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 41 through 46' Processing helix chain 'e' and resid 47 through 60 removed outlier: 3.719A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.133A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU e 102 " --> pdb=" O PHE e 98 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA e 106 " --> pdb=" O LEU e 102 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.632A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.847A 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 removed outlier: 3.943A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.372A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Proline residue: e 28 - end of helix 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: 3.723A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU f 70 " --> pdb=" O THR f 66 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.287A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 removed outlier: 3.510A pdb=" N ALA g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 34 removed outlier: 3.830A pdb=" N GLN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY g 34 " --> pdb=" O LEU g 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 29 through 34' Processing helix chain 'g' and resid 40 through 50 removed outlier: 5.400A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) 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 73 removed outlier: 5.940A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN g 66 " --> pdb=" O LEU g 62 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.853A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 4.142A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.990A 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: 3.699A pdb=" N GLN h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.711A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.531A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix No H-bonds generated for 'chain 'h' and resid 62 through 68' Processing helix chain 'h' and resid 94 through 106 removed outlier: 4.104A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 7.003A pdb=" N PHE h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU h 114 " --> pdb=" O ALA h 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 109 through 114' Processing helix chain 'i' and resid 23 through 31 removed outlier: 4.931A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY i 31 " --> pdb=" O LEU i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.588A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.513A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 113 removed outlier: 3.800A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.538A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.641A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.704A pdb=" N ARG j 95 " --> pdb=" O GLU j 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 109 removed outlier: 3.932A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.139A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 4.777A pdb=" N LYS j 72 " --> pdb=" O ASN j 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 67 through 72' Processing helix chain 'k' and resid 109 through 119 removed outlier: 5.791A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.702A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 3.686A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 83 removed outlier: 4.537A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 83' Processing helix chain 'l' and resid 93 through 99 removed outlier: 6.219A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.594A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 4.009A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.762A pdb=" N ARG n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 3.552A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.512A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.509A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.460A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 89 removed outlier: 5.161A pdb=" N SER n 89 " --> pdb=" O PRO n 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 22 removed outlier: 3.507A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR o 12 " --> pdb=" O ILE o 8 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.338A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.574A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA o 82 " --> pdb=" O VAL o 78 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.971A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG o 111 " --> pdb=" O ALA o 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 13 removed outlier: 3.638A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 5.162A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 97 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.448A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG q 10 " --> pdb=" O GLY q 6 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 30 removed outlier: 4.749A pdb=" N SER q 28 " --> pdb=" O TYR q 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 56 removed outlier: 3.534A pdb=" N ALA q 45 " --> pdb=" O ALA q 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG q 49 " --> pdb=" O ALA q 45 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 58 through 71 removed outlier: 3.810A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.537A pdb=" N ILE q 79 " --> pdb=" O TYR q 75 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.943A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP q 101 " --> pdb=" O ILE q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.608A pdb=" N THR q 106 " --> pdb=" O LYS q 102 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.656A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP s 22 " --> pdb=" O ARG s 18 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.535A pdb=" N LEU s 33 " --> pdb=" O VAL s 29 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.765A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN s 57 " --> pdb=" O SER s 53 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 3.733A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 removed outlier: 3.614A pdb=" N MET t 24 " --> pdb=" O ALA t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.711A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 4.884A 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 24 removed outlier: 4.900A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 4.024A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.929A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP x 59 " --> pdb=" O MET x 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 3.622A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.611A pdb=" N LEU y 14 " --> pdb=" O SER y 10 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET y 30 " --> pdb=" O PHE y 26 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 4.632A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.726A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA z 49 " --> pdb=" O GLY z 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.715A pdb=" N ARG B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.640A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.597A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.679A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.646A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.578A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 63 removed outlier: 3.536A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.548A pdb=" N ASN G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.309A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 3.867A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.570A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 148 removed outlier: 3.824A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 154 removed outlier: 4.292A pdb=" N MET G 153 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 154' Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.527A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 4.073A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.794A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 47 removed outlier: 4.130A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.557A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.757A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.517A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.594A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.643A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 5.644A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.588A pdb=" N ASN I 88 " --> pdb=" O ASN I 84 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 4.684A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.625A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.648A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.684A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 4.153A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 removed outlier: 3.651A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.031A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 11 through 18 removed outlier: 3.519A pdb=" N SER K 15 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 removed outlier: 3.707A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.640A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.509A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.552A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 69 removed outlier: 3.657A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 3.827A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.537A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 127 " --> pdb=" O LEU L 123 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.648A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.562A pdb=" N GLY M 16 " --> pdb=" O ARG M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 46 through 55 Proline residue: N 50 - end of helix removed outlier: 4.811A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 46 through 55' Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.617A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 5.679A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 removed outlier: 3.570A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 removed outlier: 4.253A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.723A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.790A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.844A 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 73 removed outlier: 3.954A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.651A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 removed outlier: 3.885A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.369A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.154A 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 14 through 20 removed outlier: 3.680A pdb=" N THR R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 48 through 63 removed outlier: 4.966A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.957A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.724A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 29 removed outlier: 4.542A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 46 removed outlier: 4.214A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.579A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.651A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 3.548A pdb=" N VAL T 28 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA T 43 " --> pdb=" O GLN T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 4.027A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.852A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.929A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.309A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.670A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.706A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 65 removed outlier: 3.640A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA W 57 " --> pdb=" O GLN W 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.640A pdb=" N LEU X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.544A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.221A 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 6 through 41 removed outlier: 4.877A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Y 13 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE Y 38 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.714A pdb=" N GLU Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN Y 54 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 4.248A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.777A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Y 75 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.266A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 32 removed outlier: 3.855A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.827A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.661A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG a 12 " --> pdb=" O MET a 8 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 35 removed outlier: 3.762A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.616A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.402A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 161 through 164 removed outlier: 6.499A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 89 through 95 removed outlier: 4.950A pdb=" N ASN b 89 " --> pdb=" O ALA b 105 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 3 through 7 removed outlier: 6.886A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.792A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU c 186 " --> pdb=" O ASP c 181 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 75 through 84 removed outlier: 5.423A pdb=" N ALA c 75 " --> pdb=" O LYS c 55 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG c 77 " --> pdb=" O GLY c 53 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY c 53 " --> pdb=" O ARG c 77 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU c 79 " --> pdb=" O THR c 51 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR c 51 " --> pdb=" O LEU c 79 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU c 81 " --> pdb=" O GLN c 49 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLN c 49 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG c 83 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA c 47 " --> pdb=" O ARG c 83 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY c 53 " --> pdb=" O ALA c 31 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ALA c 31 " --> pdb=" O GLY c 53 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 1 through 4 removed outlier: 4.011A pdb=" N LEU d 3 " --> pdb=" O LEU d 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU d 12 " --> pdb=" O LEU d 3 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.599A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET d 188 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU d 147 " --> pdb=" O LYS d 185 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL d 146 " --> pdb=" O LYS d 166 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG d 170 " --> pdb=" O ILE d 148 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'e' and resid 32 through 38 removed outlier: 3.579A pdb=" N CYS e 86 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'e' and resid 126 through 132 removed outlier: 3.619A pdb=" N TYR e 127 " --> pdb=" O ILE e 155 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.603A pdb=" N LYS f 26 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS f 17 " --> pdb=" O THR f 24 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 41 through 44 Processing sheet with id= 14, first strand: chain 'f' and resid 81 through 88 removed outlier: 3.764A pdb=" N LYS f 84 " --> pdb=" O LEU f 132 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU f 132 " --> pdb=" O LYS f 84 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 93 through 97 removed outlier: 3.713A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL f 112 " --> pdb=" O LEU f 104 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'g' and resid 15 through 20 removed outlier: 5.323A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'g' and resid 76 through 81 removed outlier: 5.942A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'h' and resid 24 through 28 Processing sheet with id= 19, first strand: chain 'j' and resid 52 through 56 removed outlier: 3.652A pdb=" N GLN j 138 " --> pdb=" O TRP j 15 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'j' and resid 74 through 78 removed outlier: 3.510A pdb=" N LYS j 85 " --> pdb=" O HIS j 76 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.467A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'm' and resid 38 through 41 Processing sheet with id= 23, first strand: chain 'm' and resid 62 through 65 removed outlier: 4.252A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.560A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.662A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA o 37 " --> pdb=" O ALA o 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER o 91 " --> pdb=" O THR o 24 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 37 through 44 removed outlier: 6.631A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'p' and resid 56 through 63 removed outlier: 7.174A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE p 58 " --> pdb=" O PHE p 73 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 3 through 6 removed outlier: 4.147A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS r 12 " --> pdb=" O PHE r 5 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'r' and resid 30 through 36 removed outlier: 4.321A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 's' and resid 2 through 8 removed outlier: 4.709A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 's' and resid 73 through 79 removed outlier: 3.525A pdb=" N PHE s 75 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 81 through 88 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 't' and resid 12 through 15 removed outlier: 5.351A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU t 32 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA t 83 " --> pdb=" O LEU t 32 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER t 78 " --> pdb=" O GLY t 65 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY t 65 " --> pdb=" O SER t 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'u' and resid 39 through 44 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'v' and resid 69 through 73 removed outlier: 3.693A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'w' and resid 42 through 45 removed outlier: 3.791A pdb=" N GLU w 79 " --> pdb=" O LYS w 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'w' and resid 47 through 50 removed outlier: 6.461A pdb=" N GLY w 48 " --> pdb=" O LEU w 55 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU w 55 " --> pdb=" O GLY w 48 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY w 50 " --> pdb=" O HIS w 53 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.670A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'x' and resid 33 through 38 Processing sheet with id= 40, first strand: chain 'z' and resid 33 through 38 removed outlier: 4.356A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN z 8 " --> pdb=" O HIS z 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL z 35 " --> pdb=" O ILE z 6 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.363A pdb=" N SER B 28 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 36 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP B 30 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.704A pdb=" N THR C 22 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 10 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C 20 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 34 through 39 removed outlier: 3.845A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 48 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 37 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 46 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'F' and resid 14 through 19 removed outlier: 3.987A pdb=" N LYS F 15 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F 26 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL F 17 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 24 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 19 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE F 23 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS F 27 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N HIS F 33 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 14 through 17 removed outlier: 4.387A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 66 through 70 Processing sheet with id= 47, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.561A pdb=" N GLN H 99 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.781A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'I' and resid 140 through 144 removed outlier: 6.949A pdb=" N MET I 177 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 11 through 15 removed outlier: 3.687A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 37 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 16 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 83 through 87 removed outlier: 3.539A pdb=" N GLY J 86 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA J 98 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN J 121 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 58 through 65 removed outlier: 6.208A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 54, first strand: chain 'M' and resid 22 through 27 removed outlier: 7.231A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.641A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.042A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 44 through 50 removed outlier: 3.662A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL O 74 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 29 through 34 Processing sheet with id= 59, first strand: chain 'Q' and resid 28 through 31 removed outlier: 3.646A pdb=" N LYS Q 29 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 35 through 38 removed outlier: 4.876A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 3 through 10 Processing sheet with id= 62, first strand: chain 'U' and resid 37 through 40 removed outlier: 3.522A pdb=" N ASN U 40 " --> pdb=" O GLY U 49 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'V' and resid 6 through 11 removed outlier: 3.643A pdb=" N ASP V 56 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR V 73 " --> pdb=" O ARG V 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 19 through 29 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'X' and resid 45 through 49 removed outlier: 4.149A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'a' and resid 60 through 65 removed outlier: 5.077A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 169 through 174 removed outlier: 6.518A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR a 173 " --> pdb=" O VAL a 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) 1540 hydrogen bonds defined for protein. 4533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3507 hydrogen bonds 5756 hydrogen bond angles 0 basepair planarities 1416 basepair parallelities 2995 stacking parallelities Total time for adding SS restraints: 240.53 Time building geometry restraints manager: 67.62 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: 34161 1.34 - 1.47: 66460 1.47 - 1.59: 52648 1.59 - 1.71: 9592 1.71 - 1.84: 278 Bond restraints: 163139 Sorted by residual: bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.59e+00 bond pdb=" CA PRO i 21 " pdb=" C PRO i 21 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.19e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.75e+00 bond pdb=" N GLY a 159 " pdb=" CA GLY a 159 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.63e+00 bond pdb=" O5' A 31191 " pdb=" C5' A 31191 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.13e+00 ... (remaining 163134 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.95: 27088 105.95 - 112.98: 91931 112.98 - 120.00: 61757 120.00 - 127.03: 51217 127.03 - 134.05: 12089 Bond angle restraints: 244082 Sorted by residual: angle pdb=" N TYR e 6 " pdb=" CA TYR e 6 " pdb=" C TYR e 6 " ideal model delta sigma weight residual 112.90 101.38 11.52 1.31e+00 5.83e-01 7.73e+01 angle pdb=" N LEU h 117 " pdb=" CA LEU h 117 " pdb=" C LEU h 117 " ideal model delta sigma weight residual 108.90 122.48 -13.58 1.63e+00 3.76e-01 6.94e+01 angle pdb=" N ILE l 101 " pdb=" CA ILE l 101 " pdb=" C ILE l 101 " ideal model delta sigma weight residual 110.42 118.27 -7.85 9.60e-01 1.09e+00 6.69e+01 angle pdb=" N LYS Z 58 " pdb=" CA LYS Z 58 " pdb=" C LYS Z 58 " ideal model delta sigma weight residual 111.69 101.70 9.99 1.23e+00 6.61e-01 6.60e+01 angle pdb=" N ALA f 173 " pdb=" CA ALA f 173 " pdb=" C ALA f 173 " ideal model delta sigma weight residual 113.20 103.53 9.67 1.21e+00 6.83e-01 6.39e+01 ... (remaining 244077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 93698 35.98 - 71.96: 9675 71.96 - 107.94: 1200 107.94 - 143.92: 8 143.92 - 179.90: 18 Dihedral angle restraints: 104599 sinusoidal: 87439 harmonic: 17160 Sorted by residual: dihedral pdb=" C4' U 12296 " pdb=" C3' U 12296 " pdb=" C2' U 12296 " pdb=" C1' U 12296 " ideal model delta sinusoidal sigma weight residual -35.00 33.67 -68.67 1 8.00e+00 1.56e-02 9.54e+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 33.55 166.45 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 11915 " pdb=" C1' U 11915 " pdb=" N1 U 11915 " pdb=" C2 U 11915 " ideal model delta sinusoidal sigma weight residual 200.00 39.24 160.76 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 104596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 20431 0.087 - 0.174: 9909 0.174 - 0.262: 771 0.262 - 0.349: 98 0.349 - 0.436: 11 Chirality restraints: 31220 Sorted by residual: chirality pdb=" CA PRO G 181 " pdb=" N PRO G 181 " pdb=" C PRO G 181 " pdb=" CB PRO G 181 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA PRO O 43 " pdb=" N PRO O 43 " pdb=" C PRO O 43 " pdb=" CB PRO O 43 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 31217 not shown) Planarity restraints: 13080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 1 615 " 0.092 2.00e-02 2.50e+03 5.20e-02 6.08e+01 pdb=" N1 U 1 615 " -0.004 2.00e-02 2.50e+03 pdb=" C2 U 1 615 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U 1 615 " -0.031 2.00e-02 2.50e+03 pdb=" N3 U 1 615 " -0.023 2.00e-02 2.50e+03 pdb=" C4 U 1 615 " -0.023 2.00e-02 2.50e+03 pdb=" O4 U 1 615 " 0.097 2.00e-02 2.50e+03 pdb=" C5 U 1 615 " -0.050 2.00e-02 2.50e+03 pdb=" C6 U 1 615 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 3 413 " 0.090 2.00e-02 2.50e+03 3.66e-02 4.03e+01 pdb=" N9 G 3 413 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G 3 413 " -0.040 2.00e-02 2.50e+03 pdb=" N7 G 3 413 " -0.033 2.00e-02 2.50e+03 pdb=" C5 G 3 413 " -0.015 2.00e-02 2.50e+03 pdb=" C6 G 3 413 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G 3 413 " 0.053 2.00e-02 2.50e+03 pdb=" N1 G 3 413 " 0.015 2.00e-02 2.50e+03 pdb=" C2 G 3 413 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 3 413 " -0.018 2.00e-02 2.50e+03 pdb=" N3 G 3 413 " -0.025 2.00e-02 2.50e+03 pdb=" C4 G 3 413 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 372 " 0.088 2.00e-02 2.50e+03 3.63e-02 3.95e+01 pdb=" N9 G 1 372 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G 1 372 " -0.040 2.00e-02 2.50e+03 pdb=" N7 G 1 372 " -0.032 2.00e-02 2.50e+03 pdb=" C5 G 1 372 " -0.014 2.00e-02 2.50e+03 pdb=" C6 G 1 372 " 0.015 2.00e-02 2.50e+03 pdb=" O6 G 1 372 " 0.057 2.00e-02 2.50e+03 pdb=" N1 G 1 372 " 0.009 2.00e-02 2.50e+03 pdb=" C2 G 1 372 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G 1 372 " -0.014 2.00e-02 2.50e+03 pdb=" N3 G 1 372 " -0.025 2.00e-02 2.50e+03 pdb=" C4 G 1 372 " -0.025 2.00e-02 2.50e+03 ... (remaining 13077 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 16981 2.75 - 3.29: 135081 3.29 - 3.82: 296979 3.82 - 4.36: 380092 4.36 - 4.90: 507940 Nonbonded interactions: 1337073 Sorted by model distance: nonbonded pdb=" O ARG n 69 " pdb=" OG1 THR n 70 " model vdw 2.211 2.440 nonbonded pdb=" OP1 C 1 897 " pdb=" O6 G 7 19 " model vdw 2.242 3.040 nonbonded pdb=" O2' U 11130 " pdb=" OP1 G 11131 " model vdw 2.267 2.440 nonbonded pdb=" NZ LYS E 51 " pdb=" OP2 C 1 937 " model vdw 2.277 2.520 nonbonded pdb=" N MET g 1 " pdb=" OD1 ASN g 20 " model vdw 2.287 2.520 ... (remaining 1337068 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.180 Extract box with map and model: 10.970 Check model and map are aligned: 1.630 Set scattering table: 1.040 Process input model: 548.020 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 568.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 0.043 163139 Z= 0.343 Angle : 0.991 13.578 244082 Z= 0.655 Chirality : 0.083 0.436 31220 Planarity : 0.007 0.093 13080 Dihedral : 21.961 179.898 93525 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 1.91 % Allowed : 11.93 % Favored : 86.16 % Rotamer: Outliers : 0.77 % Allowed : 6.54 % Favored : 92.69 % 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: -4.97 (0.08), residues: 5919 helix: -3.66 (0.08), residues: 1721 sheet: -2.89 (0.15), residues: 868 loop : -3.29 (0.09), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP V 72 HIS 0.001 0.000 HIS j 77 PHE 0.033 0.005 PHE T 42 TYR 0.055 0.006 TYR N 5 ARG 0.006 0.001 ARG p 38 *********************** 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 1811 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1773 time to evaluate : 5.779 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 92 LEU cc_start: 0.8543 (tp) cc_final: 0.7940 (tp) REVERT: b 173 LEU cc_start: 0.8568 (mt) cc_final: 0.7838 (mp) REVERT: b 180 MET cc_start: 0.6789 (mmm) cc_final: 0.6081 (mmm) REVERT: b 186 ASP cc_start: 0.8469 (m-30) cc_final: 0.8082 (m-30) REVERT: c 39 ASP cc_start: 0.8057 (t70) cc_final: 0.7847 (t0) REVERT: c 40 LEU cc_start: 0.8086 (mp) cc_final: 0.7373 (mt) REVERT: c 56 LYS cc_start: 0.8189 (tptp) cc_final: 0.7968 (tptm) REVERT: c 84 LEU cc_start: 0.8218 (mt) cc_final: 0.7678 (mt) REVERT: d 16 GLU cc_start: 0.7983 (tt0) cc_final: 0.7445 (tp30) REVERT: d 21 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7648 (ttm110) REVERT: d 29 HIS cc_start: 0.8225 (t-90) cc_final: 0.7423 (t70) REVERT: d 73 ILE cc_start: 0.8745 (tt) cc_final: 0.8257 (tt) REVERT: d 78 TRP cc_start: 0.8406 (m-10) cc_final: 0.8175 (m-10) REVERT: d 85 PHE cc_start: 0.7170 (m-80) cc_final: 0.6515 (m-10) REVERT: d 97 ASN cc_start: 0.7602 (m110) cc_final: 0.7337 (m110) REVERT: d 111 GLU cc_start: 0.8345 (tp30) cc_final: 0.7788 (tm-30) REVERT: d 147 LEU cc_start: 0.7820 (tt) cc_final: 0.7605 (tt) REVERT: d 171 ASP cc_start: 0.8006 (t70) cc_final: 0.7564 (t70) REVERT: d 195 GLN cc_start: 0.8724 (mt0) cc_final: 0.8416 (mm-40) REVERT: d 197 GLU cc_start: 0.7937 (tp30) cc_final: 0.7556 (tp30) REVERT: e 51 ASN cc_start: 0.9291 (m-40) cc_final: 0.8855 (p0) REVERT: e 56 LEU cc_start: 0.8653 (mt) cc_final: 0.8399 (mp) REVERT: f 61 TRP cc_start: 0.7133 (m100) cc_final: 0.6850 (m100) REVERT: f 87 GLN cc_start: 0.7971 (tt0) cc_final: 0.7383 (tp40) REVERT: g 7 ASP cc_start: 0.7872 (m-30) cc_final: 0.7212 (m-30) REVERT: h 1 MET cc_start: 0.4611 (ptt) cc_final: 0.4387 (ptt) REVERT: j 60 ASP cc_start: 0.7212 (p0) cc_final: 0.6840 (p0) REVERT: j 92 MET cc_start: 0.8025 (tpp) cc_final: 0.7694 (tpp) REVERT: j 96 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6815 (ttp-110) REVERT: j 140 LEU cc_start: 0.7335 (tp) cc_final: 0.7026 (tt) REVERT: k 5 GLN cc_start: 0.8684 (mm110) cc_final: 0.8273 (mp10) REVERT: k 12 ASP cc_start: 0.8476 (p0) cc_final: 0.7957 (p0) REVERT: k 40 LYS cc_start: 0.8969 (tppt) cc_final: 0.8594 (tppt) REVERT: l 10 GLU cc_start: 0.8508 (tp30) cc_final: 0.7861 (pm20) REVERT: l 70 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8707 (ttpt) REVERT: l 105 ILE cc_start: 0.7841 (mp) cc_final: 0.7066 (tp) REVERT: m 59 ARG cc_start: 0.6686 (tmm160) cc_final: 0.6384 (tmm-80) REVERT: m 60 GLN cc_start: 0.6147 (pt0) cc_final: 0.5590 (tp40) REVERT: m 68 PHE cc_start: 0.7893 (t80) cc_final: 0.7433 (t80) REVERT: n 24 MET cc_start: 0.8743 (ttp) cc_final: 0.8276 (ptm) REVERT: n 33 ILE cc_start: 0.6969 (tt) cc_final: 0.6663 (tt) REVERT: n 34 ILE cc_start: 0.6538 (pt) cc_final: 0.6288 (pt) REVERT: n 78 LYS cc_start: 0.7272 (tttt) cc_final: 0.6978 (tptp) REVERT: n 112 TYR cc_start: 0.7033 (m-80) cc_final: 0.6415 (m-80) REVERT: o 63 LYS cc_start: 0.8521 (tttm) cc_final: 0.8114 (ttpp) REVERT: o 65 THR cc_start: 0.6532 (p) cc_final: 0.5918 (p) REVERT: p 26 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7867 (tm-30) REVERT: p 37 LYS cc_start: 0.8639 (tttp) cc_final: 0.7985 (mmtm) REVERT: p 61 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7466 (ttt90) REVERT: p 71 ARG cc_start: 0.8691 (ttt180) cc_final: 0.7366 (ttt90) REVERT: p 86 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8865 (mtmt) REVERT: q 23 TYR cc_start: 0.7515 (m-10) cc_final: 0.7207 (m-80) REVERT: q 54 ARG cc_start: 0.8292 (mtt180) cc_final: 0.8080 (mmp-170) REVERT: q 58 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: q 71 ASN cc_start: 0.8348 (m110) cc_final: 0.8064 (m110) REVERT: q 89 ILE cc_start: 0.7908 (mt) cc_final: 0.7471 (mt) REVERT: r 35 PHE cc_start: 0.9083 (m-80) cc_final: 0.8875 (m-80) REVERT: s 1 MET cc_start: 0.7308 (tpp) cc_final: 0.6914 (tpp) REVERT: s 23 LEU cc_start: 0.8063 (mt) cc_final: 0.7835 (mp) REVERT: s 25 ARG cc_start: 0.6168 (mtt180) cc_final: 0.5617 (mtt90) REVERT: s 36 LEU cc_start: 0.8446 (mt) cc_final: 0.8175 (mt) REVERT: s 48 LYS cc_start: 0.8846 (tttt) cc_final: 0.8245 (tttp) REVERT: s 52 GLU cc_start: 0.9156 (tt0) cc_final: 0.8907 (tt0) REVERT: s 57 ASN cc_start: 0.8304 (t0) cc_final: 0.7990 (t0) REVERT: s 95 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7183 (ttp-170) REVERT: s 104 THR cc_start: 0.8451 (m) cc_final: 0.7884 (p) REVERT: t 8 LEU cc_start: 0.9149 (mt) cc_final: 0.8936 (mt) REVERT: t 33 LYS cc_start: 0.8315 (tmtt) cc_final: 0.8042 (mttt) REVERT: t 44 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8312 (tptt) REVERT: u 6 ARG cc_start: 0.6591 (tpt170) cc_final: 0.6132 (mmt-90) REVERT: u 95 PHE cc_start: 0.5865 (m-80) cc_final: 0.5460 (m-10) REVERT: v 26 PHE cc_start: 0.7800 (p90) cc_final: 0.7320 (p90) REVERT: v 81 PRO cc_start: 0.7924 (Cg_exo) cc_final: 0.7714 (Cg_endo) REVERT: w 40 LYS cc_start: 0.5537 (ttmt) cc_final: 0.5058 (ttmm) REVERT: w 46 ASN cc_start: 0.9238 (m-40) cc_final: 0.8939 (m110) REVERT: w 58 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8149 (tmmt) REVERT: x 49 ARG cc_start: 0.7960 (mtp180) cc_final: 0.6826 (mtp-110) REVERT: x 55 MET cc_start: 0.7906 (mtp) cc_final: 0.7667 (mtp) REVERT: x 73 ARG cc_start: 0.7338 (mtt180) cc_final: 0.7079 (mtt180) REVERT: y 30 MET cc_start: 0.7171 (mmp) cc_final: 0.6814 (mmp) REVERT: z 16 LEU cc_start: 0.7751 (mt) cc_final: 0.7468 (mt) REVERT: B 4 GLN cc_start: 0.8406 (tp40) cc_final: 0.8065 (tp40) REVERT: B 16 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8614 (mtt90) REVERT: B 35 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6157 (mt-10) REVERT: B 43 THR cc_start: 0.7191 (p) cc_final: 0.6982 (p) REVERT: E 2 LYS cc_start: 0.8294 (mttt) cc_final: 0.7820 (mtpt) REVERT: E 5 THR cc_start: 0.7658 (m) cc_final: 0.7425 (m) REVERT: E 29 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7366 (mmm160) REVERT: E 43 LEU cc_start: 0.8432 (mt) cc_final: 0.8149 (mt) REVERT: F 9 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8275 (tttt) REVERT: G 5 MET cc_start: 0.4315 (ttm) cc_final: 0.3359 (tpp) REVERT: G 15 PHE cc_start: 0.9233 (m-80) cc_final: 0.8686 (t80) REVERT: G 21 TYR cc_start: 0.7942 (m-80) cc_final: 0.7430 (m-80) REVERT: G 77 GLU cc_start: 0.8382 (pp20) cc_final: 0.8084 (pp20) REVERT: G 104 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8820 (mmtm) REVERT: G 107 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8437 (ptm-80) REVERT: G 137 THR cc_start: 0.9214 (p) cc_final: 0.8540 (p) REVERT: G 138 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7247 (tmm160) REVERT: G 139 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9014 (mt-10) REVERT: G 140 LEU cc_start: 0.9107 (pp) cc_final: 0.8898 (pp) REVERT: G 141 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9075 (mp0) REVERT: G 150 ILE cc_start: 0.6458 (pt) cc_final: 0.6138 (mm) REVERT: G 212 TYR cc_start: 0.8470 (m-80) cc_final: 0.8136 (m-10) REVERT: G 219 THR cc_start: 0.8997 (p) cc_final: 0.7884 (p) REVERT: G 222 GLU cc_start: 0.9094 (pt0) cc_final: 0.8846 (pp20) REVERT: H 33 ASP cc_start: 0.9141 (t0) cc_final: 0.8689 (t0) REVERT: H 42 LEU cc_start: 0.8808 (mm) cc_final: 0.8600 (mt) REVERT: H 163 ARG cc_start: 0.8047 (mpp80) cc_final: 0.7437 (mpp80) REVERT: H 184 ASN cc_start: 0.7382 (t0) cc_final: 0.7163 (t0) REVERT: H 189 HIS cc_start: 0.7848 (m90) cc_final: 0.7520 (m90) REVERT: H 200 TRP cc_start: 0.8147 (m-90) cc_final: 0.7784 (m-90) REVERT: I 61 ARG cc_start: 0.7888 (mtp85) cc_final: 0.5809 (mtp85) REVERT: I 72 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8520 (tmm-80) REVERT: I 131 ILE cc_start: 0.6262 (mm) cc_final: 0.5675 (pt) REVERT: I 171 GLU cc_start: 0.4175 (tp30) cc_final: 0.3102 (pm20) REVERT: I 195 ASN cc_start: 0.8033 (t0) cc_final: 0.7825 (t0) REVERT: J 67 ARG cc_start: 0.9065 (mtt180) cc_final: 0.8753 (mtt-85) REVERT: J 70 MET cc_start: 0.7498 (mtp) cc_final: 0.6623 (mtt) REVERT: J 110 MET cc_start: 0.7676 (mpp) cc_final: 0.7422 (mpp) REVERT: J 151 MET cc_start: 0.9402 (mmp) cc_final: 0.9114 (mmm) REVERT: J 156 ARG cc_start: 0.8185 (ptm160) cc_final: 0.7960 (ttp-170) REVERT: K 49 TYR cc_start: 0.7395 (p90) cc_final: 0.6870 (p90) REVERT: K 56 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7912 (mtmm) REVERT: K 59 TYR cc_start: 0.7444 (m-80) cc_final: 0.6693 (m-80) REVERT: K 74 LEU cc_start: 0.8709 (mp) cc_final: 0.8328 (mt) REVERT: L 34 LYS cc_start: 0.4432 (mttt) cc_final: 0.4027 (mttt) REVERT: L 51 GLN cc_start: 0.7886 (tt0) cc_final: 0.7679 (pt0) REVERT: L 73 GLU cc_start: 0.9110 (pt0) cc_final: 0.8393 (pp20) REVERT: L 128 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: M 30 LYS cc_start: 0.8891 (pttp) cc_final: 0.8574 (mtmm) REVERT: M 47 ASP cc_start: 0.8998 (t0) cc_final: 0.8654 (t0) REVERT: M 49 LYS cc_start: 0.8913 (tttt) cc_final: 0.8677 (tttm) REVERT: M 61 THR cc_start: 0.8001 (m) cc_final: 0.7618 (p) REVERT: M 63 LYS cc_start: 0.8246 (mttp) cc_final: 0.7737 (mttm) REVERT: M 85 TYR cc_start: 0.8298 (m-80) cc_final: 0.7936 (m-80) REVERT: N 20 ILE cc_start: 0.7675 (pt) cc_final: 0.7185 (mm) REVERT: N 45 MET cc_start: 0.6064 (mtm) cc_final: 0.5381 (mtm) REVERT: N 48 ARG cc_start: 0.6524 (ptt-90) cc_final: 0.5896 (ttm-80) REVERT: N 89 TYR cc_start: 0.5518 (m-80) cc_final: 0.5178 (m-80) REVERT: N 117 LEU cc_start: 0.8730 (mt) cc_final: 0.8081 (mt) REVERT: N 123 ARG cc_start: 0.8338 (mmt90) cc_final: 0.7916 (mmt-90) REVERT: O 63 ASP cc_start: 0.8879 (m-30) cc_final: 0.8298 (m-30) REVERT: O 70 HIS cc_start: 0.6926 (m90) cc_final: 0.6698 (m90) REVERT: P 39 ASN cc_start: 0.7688 (m110) cc_final: 0.7263 (m-40) REVERT: P 67 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8788 (tm-30) REVERT: P 95 THR cc_start: 0.6542 (t) cc_final: 0.5548 (t) REVERT: P 110 THR cc_start: 0.8080 (p) cc_final: 0.7364 (p) REVERT: Q 42 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7920 (ttmm) REVERT: Q 75 GLU cc_start: 0.8504 (mp0) cc_final: 0.8092 (mp0) REVERT: R 53 ASP cc_start: 0.8802 (p0) cc_final: 0.8592 (p0) REVERT: R 80 MET cc_start: 0.8825 (mtm) cc_final: 0.7688 (mtt) REVERT: R 94 LEU cc_start: 0.9276 (mt) cc_final: 0.9059 (mt) REVERT: T 52 ARG cc_start: 0.6033 (ttm170) cc_final: 0.5793 (tpp80) REVERT: U 26 ASN cc_start: 0.9162 (m-40) cc_final: 0.8943 (m-40) REVERT: U 36 VAL cc_start: 0.6250 (p) cc_final: 0.5420 (p) REVERT: U 77 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8872 (mt-10) REVERT: W 47 ARG cc_start: 0.7247 (mpt90) cc_final: 0.6977 (mmm-85) REVERT: W 59 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7466 (tptp) REVERT: Y 11 ILE cc_start: 0.9230 (mp) cc_final: 0.8685 (mp) REVERT: Y 17 ARG cc_start: 0.9173 (ptm-80) cc_final: 0.8905 (ptm-80) REVERT: Y 58 ASP cc_start: 0.8562 (m-30) cc_final: 0.8268 (m-30) REVERT: Y 69 ASN cc_start: 0.8229 (t0) cc_final: 0.8018 (t0) REVERT: Z 10 PRO cc_start: 0.4447 (OUTLIER) cc_final: 0.3440 (Cg_exo) REVERT: Z 18 PHE cc_start: 0.8539 (t80) cc_final: 0.8324 (t80) REVERT: a 210 LYS cc_start: 0.6645 (mmmt) cc_final: 0.6223 (mmmt) outliers start: 38 outliers final: 13 residues processed: 1803 average time/residue: 1.4795 time to fit residues: 4430.1218 Evaluate side-chains 1326 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1310 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain Z residue 10 PRO 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: 20.0000 chunk 273 optimal weight: 3.9990 chunk 540 optimal weight: 50.0000 chunk 428 optimal weight: 5.9990 chunk 828 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 503 optimal weight: 30.0000 chunk 616 optimal weight: 20.0000 chunk 959 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 59 GLN b 85 ASN ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 49 GLN c 130 GLN c 140 HIS c 150 GLN ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 HIS d 94 GLN d 97 ASN e 126 ASN ** f 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS f 127 GLN g 33 GLN h 4 ASN i 5 GLN i 33 ASN i 104 GLN i 110 GLN j 58 ASN j 128 ASN j 135 GLN k 93 GLN m 22 GLN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 14 GLN p 74 GLN q 43 GLN q 55 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 9 HIS s 31 GLN u 73 ASN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 ASN w 53 HIS ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 38 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 58 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN F 35 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS G 38 HIS G 50 ASN G 108 GLN G 119 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 184 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN J 60 GLN J 69 ASN J 77 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN J 145 ASN ** J 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 15 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 3 ASN N 31 GLN N 74 GLN N 125 GLN O 58 ASN P 21 HIS ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN T 39 GLN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN X 55 GLN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 165 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 163139 Z= 0.308 Angle : 0.792 10.619 244082 Z= 0.408 Chirality : 0.041 0.302 31220 Planarity : 0.006 0.072 13080 Dihedral : 23.101 175.733 81752 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.31 % Favored : 89.46 % Rotamer: Outliers : 4.67 % Allowed : 17.22 % Favored : 78.12 % 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: -3.78 (0.09), residues: 5919 helix: -2.04 (0.10), residues: 1819 sheet: -2.39 (0.16), residues: 898 loop : -2.88 (0.10), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 43 HIS 0.020 0.002 HIS Y 67 PHE 0.027 0.003 PHE J 47 TYR 0.026 0.002 TYR e 6 ARG 0.014 0.001 ARG D 34 *********************** 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 1665 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1436 time to evaluate : 6.345 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: b 47 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7020 (mmt90) REVERT: b 173 LEU cc_start: 0.8800 (mt) cc_final: 0.8531 (mm) REVERT: b 180 MET cc_start: 0.6691 (mmm) cc_final: 0.5904 (mmm) REVERT: b 186 ASP cc_start: 0.8625 (m-30) cc_final: 0.8158 (m-30) REVERT: b 193 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: c 26 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8841 (m) REVERT: c 40 LEU cc_start: 0.8057 (mp) cc_final: 0.7505 (mt) REVERT: c 56 LYS cc_start: 0.8435 (tptp) cc_final: 0.8150 (tptp) REVERT: c 127 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: c 188 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8378 (mm) REVERT: d 21 ARG cc_start: 0.8581 (ttm170) cc_final: 0.7837 (ttm110) REVERT: d 29 HIS cc_start: 0.8109 (t-90) cc_final: 0.7189 (t70) REVERT: d 61 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7869 (ptp90) REVERT: d 73 ILE cc_start: 0.8909 (tt) cc_final: 0.8327 (tt) REVERT: d 78 TRP cc_start: 0.8501 (m-10) cc_final: 0.8248 (m-10) REVERT: d 85 PHE cc_start: 0.7504 (m-80) cc_final: 0.6550 (m-10) REVERT: d 97 ASN cc_start: 0.7810 (m-40) cc_final: 0.7604 (m-40) REVERT: d 101 TYR cc_start: 0.8539 (t80) cc_final: 0.8315 (t80) REVERT: e 25 MET cc_start: 0.8614 (tpt) cc_final: 0.8178 (ttm) REVERT: e 56 LEU cc_start: 0.8260 (mt) cc_final: 0.7701 (mt) REVERT: e 112 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7166 (t70) REVERT: e 152 ASP cc_start: 0.5862 (OUTLIER) cc_final: 0.5308 (m-30) REVERT: f 41 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8694 (tm-30) REVERT: f 61 TRP cc_start: 0.6822 (m100) cc_final: 0.6553 (m100) REVERT: f 104 LEU cc_start: 0.9325 (tp) cc_final: 0.9106 (tt) REVERT: f 114 HIS cc_start: 0.8399 (t70) cc_final: 0.8019 (t-90) REVERT: f 123 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7365 (tm-30) REVERT: g 7 ASP cc_start: 0.7981 (m-30) cc_final: 0.7290 (m-30) REVERT: i 133 ARG cc_start: 0.6570 (ttm110) cc_final: 0.5459 (ttp80) REVERT: j 40 HIS cc_start: 0.8134 (p-80) cc_final: 0.7638 (p-80) REVERT: j 69 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7402 (tpp-160) REVERT: j 76 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7672 (p-80) REVERT: j 78 THR cc_start: 0.8318 (p) cc_final: 0.8117 (t) REVERT: j 92 MET cc_start: 0.8205 (tpp) cc_final: 0.7792 (tpp) REVERT: j 113 PRO cc_start: 0.8152 (Cg_endo) cc_final: 0.7920 (Cg_exo) REVERT: j 140 LEU cc_start: 0.7524 (tp) cc_final: 0.7191 (tt) REVERT: k 4 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8035 (mt-10) REVERT: k 5 GLN cc_start: 0.9000 (mm110) cc_final: 0.8539 (mp10) REVERT: k 12 ASP cc_start: 0.8459 (p0) cc_final: 0.8000 (p0) REVERT: k 40 LYS cc_start: 0.9190 (tppt) cc_final: 0.8859 (tppt) REVERT: k 113 MET cc_start: 0.7780 (mmm) cc_final: 0.7368 (mmm) REVERT: l 10 GLU cc_start: 0.8740 (tp30) cc_final: 0.7799 (pp20) REVERT: l 55 MET cc_start: 0.7987 (mmt) cc_final: 0.7665 (tpp) REVERT: l 59 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6722 (mmm-85) REVERT: l 70 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8770 (ttpt) REVERT: l 125 LEU cc_start: 0.6167 (mt) cc_final: 0.5961 (mp) REVERT: m 59 ARG cc_start: 0.7130 (tmm160) cc_final: 0.6894 (ttp80) REVERT: m 60 GLN cc_start: 0.6132 (pt0) cc_final: 0.5632 (tp40) REVERT: m 68 PHE cc_start: 0.8138 (t80) cc_final: 0.7840 (t80) REVERT: n 4 ARG cc_start: 0.8716 (mmm160) cc_final: 0.7971 (mmm160) REVERT: n 12 ARG cc_start: 0.7375 (mtt90) cc_final: 0.6262 (ttm110) REVERT: n 24 MET cc_start: 0.8766 (ttp) cc_final: 0.8296 (ptm) REVERT: n 45 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7090 (mtp85) REVERT: n 49 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7794 (mm-30) REVERT: n 82 GLU cc_start: 0.8009 (pt0) cc_final: 0.7514 (pm20) REVERT: n 110 MET cc_start: 0.6807 (mtm) cc_final: 0.6484 (mtm) REVERT: n 112 TYR cc_start: 0.7731 (m-80) cc_final: 0.7119 (m-80) REVERT: o 18 LEU cc_start: 0.8362 (tt) cc_final: 0.8112 (mm) REVERT: o 20 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7163 (mm-30) REVERT: o 93 ASP cc_start: 0.7082 (t70) cc_final: 0.6337 (t0) REVERT: p 26 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8113 (tm-30) REVERT: p 61 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7672 (ttt90) REVERT: p 71 ARG cc_start: 0.8650 (ttt180) cc_final: 0.7245 (ttt90) REVERT: p 112 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5906 (mtp180) REVERT: q 23 TYR cc_start: 0.7351 (m-10) cc_final: 0.6774 (m-80) REVERT: q 49 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: q 52 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7127 (ttm170) REVERT: r 54 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6679 (t) REVERT: r 86 GLN cc_start: 0.8747 (tp-100) cc_final: 0.7322 (tt0) REVERT: s 17 VAL cc_start: 0.8653 (t) cc_final: 0.8371 (t) REVERT: s 95 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7239 (ttp-170) REVERT: s 104 THR cc_start: 0.8558 (m) cc_final: 0.7784 (p) REVERT: t 56 GLU cc_start: 0.7708 (mp0) cc_final: 0.7320 (mp0) REVERT: t 87 LEU cc_start: 0.8104 (tp) cc_final: 0.7526 (tp) REVERT: u 93 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6876 (mtm180) REVERT: u 95 PHE cc_start: 0.5552 (m-80) cc_final: 0.5145 (m-10) REVERT: v 2 PHE cc_start: 0.5310 (m-80) cc_final: 0.4311 (m-10) REVERT: v 26 PHE cc_start: 0.7304 (p90) cc_final: 0.7101 (p90) REVERT: v 40 ILE cc_start: 0.8003 (mm) cc_final: 0.7287 (mt) REVERT: v 55 GLU cc_start: 0.7782 (pm20) cc_final: 0.7482 (pm20) REVERT: v 56 PHE cc_start: 0.7666 (t80) cc_final: 0.6764 (t80) REVERT: v 87 GLN cc_start: 0.7633 (pm20) cc_final: 0.7091 (pp30) REVERT: v 88 HIS cc_start: 0.7010 (t-90) cc_final: 0.6676 (t-170) REVERT: w 33 ILE cc_start: 0.8753 (tp) cc_final: 0.8537 (tp) REVERT: w 46 ASN cc_start: 0.9201 (m-40) cc_final: 0.8878 (m110) REVERT: w 73 ARG cc_start: 0.8138 (ptp-170) cc_final: 0.7762 (ptp-170) REVERT: x 49 ARG cc_start: 0.8176 (mtp180) cc_final: 0.6980 (mtp-110) REVERT: x 55 MET cc_start: 0.8197 (mtp) cc_final: 0.7979 (mtt) REVERT: y 1 MET cc_start: 0.8417 (mtm) cc_final: 0.8211 (mtm) REVERT: y 26 PHE cc_start: 0.8542 (t80) cc_final: 0.8313 (t80) REVERT: y 30 MET cc_start: 0.7599 (mmp) cc_final: 0.7396 (mmp) REVERT: z 44 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8609 (mmm160) REVERT: B 16 ARG cc_start: 0.9249 (mtt180) cc_final: 0.8491 (mtt90) REVERT: E 2 LYS cc_start: 0.8409 (mttt) cc_final: 0.8038 (mttt) REVERT: E 29 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7940 (mmm160) REVERT: E 43 LEU cc_start: 0.8647 (mt) cc_final: 0.8277 (mt) REVERT: G 15 PHE cc_start: 0.9232 (m-80) cc_final: 0.8817 (t80) REVERT: G 21 TYR cc_start: 0.8080 (m-80) cc_final: 0.7588 (m-80) REVERT: G 23 ASN cc_start: 0.6543 (t0) cc_final: 0.6302 (p0) REVERT: G 38 HIS cc_start: 0.6723 (m-70) cc_final: 0.6493 (m-70) REVERT: G 41 ASN cc_start: 0.7791 (t0) cc_final: 0.6906 (m-40) REVERT: G 48 MET cc_start: 0.9505 (mpp) cc_final: 0.8968 (mpp) REVERT: G 77 GLU cc_start: 0.8362 (pp20) cc_final: 0.7503 (pp20) REVERT: G 80 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8164 (tmmt) REVERT: G 103 TRP cc_start: 0.8891 (t-100) cc_final: 0.8486 (t-100) REVERT: G 104 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8841 (mmtt) REVERT: G 137 THR cc_start: 0.9245 (p) cc_final: 0.8978 (p) REVERT: G 138 ARG cc_start: 0.8210 (mtm110) cc_final: 0.6908 (tpt90) REVERT: G 173 LYS cc_start: 0.9019 (tttt) cc_final: 0.8623 (pttp) REVERT: G 211 LEU cc_start: 0.9361 (tt) cc_final: 0.9158 (mt) REVERT: G 212 TYR cc_start: 0.8546 (m-10) cc_final: 0.8344 (m-10) REVERT: G 219 THR cc_start: 0.9203 (p) cc_final: 0.8240 (p) REVERT: G 222 GLU cc_start: 0.8886 (pt0) cc_final: 0.8639 (pp20) REVERT: H 11 LEU cc_start: 0.8219 (mt) cc_final: 0.7955 (mt) REVERT: H 39 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7779 (ttt-90) REVERT: H 125 ARG cc_start: 0.8929 (mtm180) cc_final: 0.8590 (mtm180) REVERT: H 129 PHE cc_start: 0.8401 (p90) cc_final: 0.8146 (p90) REVERT: H 138 GLN cc_start: 0.8927 (tp40) cc_final: 0.8386 (tm-30) REVERT: H 169 GLU cc_start: 0.8384 (tp30) cc_final: 0.7889 (tm-30) REVERT: H 174 LEU cc_start: 0.7615 (mm) cc_final: 0.7025 (tp) REVERT: H 183 TYR cc_start: 0.5270 (t80) cc_final: 0.5008 (t80) REVERT: H 189 HIS cc_start: 0.8175 (m90) cc_final: 0.7820 (m90) REVERT: I 72 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8682 (tmm-80) REVERT: I 74 TYR cc_start: 0.7769 (m-80) cc_final: 0.7006 (m-80) REVERT: I 170 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5420 (pp) REVERT: I 171 GLU cc_start: 0.4392 (tp30) cc_final: 0.4115 (pm20) REVERT: I 195 ASN cc_start: 0.8200 (t0) cc_final: 0.7885 (t0) REVERT: J 70 MET cc_start: 0.8110 (mtp) cc_final: 0.7727 (mtt) REVERT: J 92 ARG cc_start: 0.7455 (mtm180) cc_final: 0.6952 (mtm180) REVERT: J 110 MET cc_start: 0.7784 (mpp) cc_final: 0.7006 (mpp) REVERT: J 133 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6402 (tp) REVERT: J 150 GLU cc_start: 0.8719 (tp30) cc_final: 0.8443 (tp30) REVERT: J 151 MET cc_start: 0.9377 (mmp) cc_final: 0.9111 (mmm) REVERT: K 1 MET cc_start: 0.8266 (mtm) cc_final: 0.7417 (mtp) REVERT: K 33 GLU cc_start: 0.8310 (pm20) cc_final: 0.8076 (pp20) REVERT: L 73 GLU cc_start: 0.9136 (pt0) cc_final: 0.8576 (pm20) REVERT: L 96 ASN cc_start: 0.9275 (p0) cc_final: 0.8984 (p0) REVERT: L 143 MET cc_start: 0.8666 (mtt) cc_final: 0.8311 (mmp) REVERT: M 14 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6677 (mtp180) REVERT: M 49 LYS cc_start: 0.8981 (tttt) cc_final: 0.8674 (tttp) REVERT: M 61 THR cc_start: 0.8444 (m) cc_final: 0.8085 (p) REVERT: M 63 LYS cc_start: 0.7806 (mttp) cc_final: 0.7187 (mttm) REVERT: N 45 MET cc_start: 0.6213 (mtm) cc_final: 0.5725 (mtm) REVERT: N 48 ARG cc_start: 0.6801 (ptt-90) cc_final: 0.6008 (ttm-80) REVERT: N 86 LEU cc_start: 0.6903 (mt) cc_final: 0.6483 (pp) REVERT: N 89 TYR cc_start: 0.5617 (m-80) cc_final: 0.5125 (m-80) REVERT: O 62 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.7145 (ttm110) REVERT: O 63 ASP cc_start: 0.8801 (m-30) cc_final: 0.8381 (m-30) REVERT: P 17 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8184 (p0) REVERT: P 39 ASN cc_start: 0.7960 (m110) cc_final: 0.7557 (m110) REVERT: P 92 ARG cc_start: 0.6247 (ttp-170) cc_final: 0.5680 (tmm-80) REVERT: Q 75 GLU cc_start: 0.8441 (mp0) cc_final: 0.7924 (mp0) REVERT: Q 89 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8858 (mp) REVERT: Q 116 TYR cc_start: 0.7726 (m-80) cc_final: 0.7277 (m-10) REVERT: R 49 GLU cc_start: 0.8200 (tp30) cc_final: 0.7743 (tp30) REVERT: R 53 ASP cc_start: 0.8576 (p0) cc_final: 0.8323 (p0) REVERT: S 20 PHE cc_start: 0.5338 (m-10) cc_final: 0.4219 (m-10) REVERT: T 36 ASN cc_start: 0.7703 (m110) cc_final: 0.7251 (m-40) REVERT: T 57 ARG cc_start: 0.8282 (ppt170) cc_final: 0.7668 (mpt180) REVERT: T 67 ASP cc_start: 0.8454 (m-30) cc_final: 0.8206 (t70) REVERT: U 5 ARG cc_start: 0.7085 (ptt180) cc_final: 0.6399 (mtm180) REVERT: U 25 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7922 (ttm-80) REVERT: U 26 ASN cc_start: 0.9181 (m-40) cc_final: 0.8923 (m-40) REVERT: U 77 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8869 (mt-10) REVERT: W 47 ARG cc_start: 0.7245 (mpt90) cc_final: 0.6959 (mmm-85) REVERT: W 59 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7825 (tptp) REVERT: Y 11 ILE cc_start: 0.8927 (mp) cc_final: 0.8550 (mp) REVERT: Y 17 ARG cc_start: 0.9141 (ptm-80) cc_final: 0.8435 (ttp80) REVERT: Y 58 ASP cc_start: 0.8403 (m-30) cc_final: 0.8183 (m-30) REVERT: Y 70 LYS cc_start: 0.9398 (tttm) cc_final: 0.7989 (mmtm) REVERT: Y 74 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7775 (m-70) REVERT: Z 11 PHE cc_start: 0.7087 (p90) cc_final: 0.6725 (p90) REVERT: Z 12 ASP cc_start: 0.8326 (t0) cc_final: 0.8010 (t0) REVERT: Z 36 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: a 210 LYS cc_start: 0.6734 (mmmt) cc_final: 0.6339 (mmmt) outliers start: 229 outliers final: 138 residues processed: 1552 average time/residue: 1.4146 time to fit residues: 3687.3340 Evaluate side-chains 1438 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1284 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 259 ASN Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 179 SER Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 91 SER Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 54 VAL Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 100 GLU Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 53 MET Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 65 TYR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 33 TRP Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Z residue 36 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 20.0000 chunk 856 optimal weight: 10.0000 chunk 953 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 771 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN f 19 ASN f 87 GLN ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 GLN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 38 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 70 GLN I 73 ASN J 69 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN S 61 ASN T 19 ASN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN W 18 GLN ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 160 GLN a 203 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 163139 Z= 0.373 Angle : 0.850 12.651 244082 Z= 0.432 Chirality : 0.044 0.510 31220 Planarity : 0.007 0.069 13080 Dihedral : 23.845 177.018 81735 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.62 % Favored : 87.19 % Rotamer: Outliers : 6.85 % Allowed : 20.62 % Favored : 72.53 % Cbeta Deviations : 0.02 % 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: -3.47 (0.10), residues: 5919 helix: -1.59 (0.11), residues: 1810 sheet: -2.32 (0.16), residues: 894 loop : -2.80 (0.10), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP P 43 HIS 0.062 0.003 HIS Y 74 PHE 0.041 0.003 PHE T 42 TYR 0.028 0.003 TYR f 163 ARG 0.029 0.001 ARG L 95 *********************** 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 1694 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1358 time to evaluate : 6.364 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: b 23 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6848 (mm) REVERT: b 47 ARG cc_start: 0.8553 (mtt180) cc_final: 0.7092 (mmt90) REVERT: b 81 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: b 166 ARG cc_start: 0.8316 (ptp90) cc_final: 0.7949 (ptp90) REVERT: b 237 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7051 (mtt180) REVERT: b 263 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: c 26 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8869 (m) REVERT: c 40 LEU cc_start: 0.8131 (mp) cc_final: 0.7761 (mt) REVERT: c 56 LYS cc_start: 0.8602 (tptp) cc_final: 0.8397 (tptp) REVERT: c 127 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: c 188 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8268 (mm) REVERT: d 29 HIS cc_start: 0.8133 (t-90) cc_final: 0.7237 (t70) REVERT: d 61 ARG cc_start: 0.8151 (mpp-170) cc_final: 0.7861 (ptp90) REVERT: d 63 LYS cc_start: 0.5963 (mtmt) cc_final: 0.5707 (mtmt) REVERT: d 73 ILE cc_start: 0.8808 (tt) cc_final: 0.8297 (tt) REVERT: d 78 TRP cc_start: 0.8523 (m-10) cc_final: 0.8265 (m-10) REVERT: d 112 LEU cc_start: 0.9487 (mt) cc_final: 0.9266 (mt) REVERT: e 51 ASN cc_start: 0.9240 (m-40) cc_final: 0.8742 (p0) REVERT: e 95 MET cc_start: 0.7909 (ptm) cc_final: 0.7524 (ptt) REVERT: e 112 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7320 (t70) REVERT: e 140 ILE cc_start: 0.5507 (mt) cc_final: 0.5099 (mp) REVERT: e 152 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: f 123 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7466 (tm-30) REVERT: g 7 ASP cc_start: 0.8034 (m-30) cc_final: 0.7462 (m-30) REVERT: i 133 ARG cc_start: 0.6580 (ttm110) cc_final: 0.5183 (ttp80) REVERT: j 40 HIS cc_start: 0.8157 (p-80) cc_final: 0.7792 (p-80) REVERT: j 69 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7654 (tpp-160) REVERT: j 76 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7683 (p-80) REVERT: j 98 GLU cc_start: 0.8512 (pm20) cc_final: 0.8107 (pm20) REVERT: j 108 MET cc_start: 0.8297 (mtp) cc_final: 0.7783 (mmm) REVERT: j 116 ARG cc_start: 0.6734 (tpt-90) cc_final: 0.6525 (ttt180) REVERT: j 140 LEU cc_start: 0.7261 (tp) cc_final: 0.7012 (tt) REVERT: k 7 MET cc_start: 0.8067 (tpp) cc_final: 0.7538 (tpt) REVERT: k 12 ASP cc_start: 0.8516 (p0) cc_final: 0.8148 (p0) REVERT: k 40 LYS cc_start: 0.9326 (tppt) cc_final: 0.8911 (tptp) REVERT: k 98 ARG cc_start: 0.7062 (mmt180) cc_final: 0.6372 (tpp-160) REVERT: k 113 MET cc_start: 0.8295 (mmm) cc_final: 0.7806 (mmm) REVERT: l 10 GLU cc_start: 0.8778 (tp30) cc_final: 0.7823 (pp20) REVERT: l 55 MET cc_start: 0.8310 (mmt) cc_final: 0.7991 (tpp) REVERT: m 22 GLN cc_start: 0.1753 (OUTLIER) cc_final: 0.1236 (pt0) REVERT: m 60 GLN cc_start: 0.5830 (pt0) cc_final: 0.5444 (tp40) REVERT: m 68 PHE cc_start: 0.8253 (t80) cc_final: 0.8019 (t80) REVERT: n 13 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8394 (p0) REVERT: n 24 MET cc_start: 0.8687 (ttp) cc_final: 0.8450 (ptm) REVERT: n 49 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8126 (mm-30) REVERT: n 112 TYR cc_start: 0.7703 (m-80) cc_final: 0.7047 (m-80) REVERT: o 18 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7872 (mm) REVERT: o 63 LYS cc_start: 0.8468 (tttm) cc_final: 0.8187 (tttp) REVERT: o 67 ASN cc_start: 0.7936 (t0) cc_final: 0.7603 (m-40) REVERT: p 61 ARG cc_start: 0.8067 (ttt90) cc_final: 0.7600 (ttt90) REVERT: p 71 ARG cc_start: 0.8493 (ttt180) cc_final: 0.7217 (ttt90) REVERT: q 5 ARG cc_start: 0.7755 (ptt90) cc_final: 0.7166 (ptt-90) REVERT: q 49 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: q 54 ARG cc_start: 0.7498 (mmp-170) cc_final: 0.7169 (mmp-170) REVERT: q 56 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.6223 (m-10) REVERT: q 90 ASP cc_start: 0.8243 (p0) cc_final: 0.7987 (p0) REVERT: s 15 GLN cc_start: 0.8192 (mt0) cc_final: 0.7984 (mt0) REVERT: s 17 VAL cc_start: 0.8787 (t) cc_final: 0.8536 (t) REVERT: s 48 LYS cc_start: 0.9024 (tttt) cc_final: 0.8592 (tttp) REVERT: s 74 ILE cc_start: 0.8456 (tt) cc_final: 0.8230 (tt) REVERT: s 95 ARG cc_start: 0.7561 (ttp-170) cc_final: 0.6954 (ttp-170) REVERT: t 56 GLU cc_start: 0.7784 (mp0) cc_final: 0.7338 (mp0) REVERT: t 87 LEU cc_start: 0.7940 (tp) cc_final: 0.7382 (tp) REVERT: u 97 SER cc_start: 0.8371 (t) cc_final: 0.7910 (p) REVERT: v 2 PHE cc_start: 0.6252 (m-80) cc_final: 0.5048 (m-80) REVERT: v 26 PHE cc_start: 0.7452 (p90) cc_final: 0.7097 (p90) REVERT: v 40 ILE cc_start: 0.7374 (mm) cc_final: 0.6802 (mt) REVERT: v 50 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: v 56 PHE cc_start: 0.7476 (t80) cc_final: 0.7028 (t80) REVERT: v 87 GLN cc_start: 0.7510 (pm20) cc_final: 0.7227 (pm20) REVERT: y 5 GLU cc_start: 0.7860 (tp30) cc_final: 0.7577 (tp30) REVERT: y 26 PHE cc_start: 0.8494 (t80) cc_final: 0.8207 (t80) REVERT: B 16 ARG cc_start: 0.9268 (mtt180) cc_final: 0.8509 (mtt90) REVERT: B 39 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7290 (mtp85) REVERT: C 21 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7727 (p) REVERT: E 2 LYS cc_start: 0.8350 (mttt) cc_final: 0.7861 (mtpt) REVERT: G 15 PHE cc_start: 0.9295 (m-80) cc_final: 0.8892 (t80) REVERT: G 19 THR cc_start: 0.2365 (OUTLIER) cc_final: 0.2149 (p) REVERT: G 21 TYR cc_start: 0.8122 (m-80) cc_final: 0.7554 (m-80) REVERT: G 77 GLU cc_start: 0.8488 (pp20) cc_final: 0.8007 (pp20) REVERT: G 80 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8303 (tmmt) REVERT: G 103 TRP cc_start: 0.8702 (t-100) cc_final: 0.8329 (t-100) REVERT: G 173 LYS cc_start: 0.8958 (tttt) cc_final: 0.8585 (pttp) REVERT: G 211 LEU cc_start: 0.9470 (tt) cc_final: 0.9228 (mt) REVERT: G 219 THR cc_start: 0.9231 (p) cc_final: 0.8442 (p) REVERT: H 39 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8168 (ttt-90) REVERT: H 54 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7481 (pt) REVERT: H 125 ARG cc_start: 0.8948 (mtm180) cc_final: 0.8655 (mtm180) REVERT: H 129 PHE cc_start: 0.8449 (p90) cc_final: 0.8129 (p90) REVERT: H 138 GLN cc_start: 0.8966 (tp40) cc_final: 0.8483 (tm-30) REVERT: H 163 ARG cc_start: 0.8228 (mpp80) cc_final: 0.7584 (mpp80) REVERT: H 169 GLU cc_start: 0.8412 (tp30) cc_final: 0.7791 (tm-30) REVERT: I 74 TYR cc_start: 0.7872 (m-80) cc_final: 0.7262 (m-80) REVERT: I 162 GLU cc_start: 0.8817 (tp30) cc_final: 0.8472 (mp0) REVERT: I 195 ASN cc_start: 0.8176 (t0) cc_final: 0.7824 (t0) REVERT: J 25 LYS cc_start: 0.8072 (tptt) cc_final: 0.7601 (tptp) REVERT: J 70 MET cc_start: 0.8268 (mtp) cc_final: 0.7985 (mtt) REVERT: J 150 GLU cc_start: 0.8716 (tp30) cc_final: 0.8401 (tp30) REVERT: J 151 MET cc_start: 0.9387 (mmp) cc_final: 0.9031 (mmm) REVERT: K 46 GLN cc_start: 0.9084 (mt0) cc_final: 0.8363 (mt0) REVERT: L 55 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8457 (ptpp) REVERT: L 73 GLU cc_start: 0.9234 (pt0) cc_final: 0.8469 (pp20) REVERT: L 89 GLU cc_start: 0.8157 (tp30) cc_final: 0.7618 (tp30) REVERT: L 143 MET cc_start: 0.8568 (mtt) cc_final: 0.8276 (mmp) REVERT: M 14 ARG cc_start: 0.7442 (ttm110) cc_final: 0.6648 (mtp180) REVERT: M 45 ILE cc_start: 0.8284 (mt) cc_final: 0.8063 (mp) REVERT: M 47 ASP cc_start: 0.8533 (t0) cc_final: 0.7861 (t0) REVERT: M 49 LYS cc_start: 0.9025 (tttt) cc_final: 0.8737 (tttp) REVERT: M 63 LYS cc_start: 0.8076 (mttp) cc_final: 0.7608 (mttm) REVERT: M 86 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7184 (mmmt) REVERT: M 90 GLU cc_start: 0.7939 (tt0) cc_final: 0.7552 (tm-30) REVERT: N 48 ARG cc_start: 0.6914 (ptt-90) cc_final: 0.6197 (ttm-80) REVERT: N 49 GLN cc_start: 0.8726 (tt0) cc_final: 0.8356 (tt0) REVERT: N 89 TYR cc_start: 0.5156 (m-80) cc_final: 0.4733 (m-80) REVERT: N 117 LEU cc_start: 0.8813 (mt) cc_final: 0.8494 (tp) REVERT: N 123 ARG cc_start: 0.8335 (mmt90) cc_final: 0.7958 (mmt-90) REVERT: O 63 ASP cc_start: 0.8612 (m-30) cc_final: 0.8151 (m-30) REVERT: P 39 ASN cc_start: 0.8087 (m110) cc_final: 0.7698 (m110) REVERT: P 45 THR cc_start: 0.6759 (OUTLIER) cc_final: 0.6524 (t) REVERT: P 92 ARG cc_start: 0.5791 (ttp-170) cc_final: 0.5169 (tmm-80) REVERT: Q 116 TYR cc_start: 0.8314 (m-80) cc_final: 0.8047 (m-10) REVERT: R 49 GLU cc_start: 0.7990 (tp30) cc_final: 0.7632 (tp30) REVERT: R 53 ASP cc_start: 0.8575 (p0) cc_final: 0.8358 (p0) REVERT: R 102 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8609 (ttpp) REVERT: S 52 ARG cc_start: 0.8337 (tpt170) cc_final: 0.6808 (tpp80) REVERT: T 19 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8053 (t0) REVERT: T 58 MET cc_start: 0.8465 (tmm) cc_final: 0.8167 (tmm) REVERT: U 25 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7946 (ttm-80) REVERT: U 51 ARG cc_start: 0.8371 (mtm180) cc_final: 0.7870 (mtm180) REVERT: U 77 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8910 (mt-10) REVERT: V 36 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6424 (t80) REVERT: W 47 ARG cc_start: 0.7380 (mpt90) cc_final: 0.6926 (mmm-85) REVERT: W 52 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8262 (ttm170) REVERT: W 54 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7907 (tp) REVERT: W 59 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7525 (tptp) REVERT: X 31 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8133 (tmm-80) REVERT: X 33 TRP cc_start: 0.6124 (OUTLIER) cc_final: 0.5570 (m-10) REVERT: Y 17 ARG cc_start: 0.9073 (ptm-80) cc_final: 0.8672 (ptm-80) REVERT: Y 24 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6520 (mtt180) REVERT: Y 69 ASN cc_start: 0.7535 (t0) cc_final: 0.7312 (t0) REVERT: Y 70 LYS cc_start: 0.9393 (tttm) cc_final: 0.8550 (tppt) REVERT: Z 12 ASP cc_start: 0.8316 (t0) cc_final: 0.7979 (t0) REVERT: Z 38 GLU cc_start: 0.8176 (tp30) cc_final: 0.7876 (tp30) outliers start: 336 outliers final: 209 residues processed: 1544 average time/residue: 1.4021 time to fit residues: 3644.0999 Evaluate side-chains 1476 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1244 time to evaluate : 6.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 84 GLU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 91 ARG Chi-restraints excluded: chain r residue 13 ARG Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 50 MET Chi-restraints excluded: chain v residue 51 GLN Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 141 HIS Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 70 HIS Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 19 ASN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 33 TRP Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 50 ILE 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: 8.9990 chunk 106 optimal weight: 40.0000 chunk 458 optimal weight: 30.0000 chunk 645 optimal weight: 20.0000 chunk 965 optimal weight: 9.9990 chunk 1021 optimal weight: 10.0000 chunk 504 optimal weight: 9.9990 chunk 914 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 55 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN E 25 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 70 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** U 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 163139 Z= 0.410 Angle : 0.900 13.063 244082 Z= 0.453 Chirality : 0.047 0.337 31220 Planarity : 0.007 0.099 13080 Dihedral : 24.357 179.555 81732 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 39.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.50 % Favored : 87.31 % Rotamer: Outliers : 8.60 % Allowed : 22.43 % Favored : 68.97 % Cbeta Deviations : 0.02 % 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: -3.48 (0.10), residues: 5919 helix: -1.53 (0.11), residues: 1783 sheet: -2.37 (0.16), residues: 906 loop : -2.82 (0.10), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP P 43 HIS 0.044 0.003 HIS Y 74 PHE 0.032 0.003 PHE Z 36 TYR 0.025 0.003 TYR d 35 ARG 0.018 0.001 ARG q 54 *********************** 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 1715 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 422 poor density : 1293 time to evaluate : 6.427 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: b 23 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (mm) REVERT: b 47 ARG cc_start: 0.8588 (mtt180) cc_final: 0.7085 (mmt90) REVERT: b 57 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7047 (t-90) REVERT: b 166 ARG cc_start: 0.8410 (ptp90) cc_final: 0.8029 (ptp90) REVERT: b 186 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: b 237 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7374 (mtt180) REVERT: b 263 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: c 2 ILE cc_start: 0.6825 (pt) cc_final: 0.6620 (pt) REVERT: c 26 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8852 (m) REVERT: c 40 LEU cc_start: 0.8253 (mp) cc_final: 0.7851 (mt) REVERT: c 127 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7767 (m-10) REVERT: c 183 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8493 (pp20) REVERT: c 188 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8428 (mm) REVERT: d 29 HIS cc_start: 0.8142 (t-90) cc_final: 0.7269 (t70) REVERT: d 61 ARG cc_start: 0.8156 (mpp-170) cc_final: 0.7858 (ptp90) REVERT: d 63 LYS cc_start: 0.6165 (mtmt) cc_final: 0.5869 (mtmt) REVERT: d 73 ILE cc_start: 0.8950 (tt) cc_final: 0.8338 (tt) REVERT: d 78 TRP cc_start: 0.8547 (m-10) cc_final: 0.8261 (m-10) REVERT: d 101 TYR cc_start: 0.8240 (t80) cc_final: 0.7758 (t80) REVERT: d 112 LEU cc_start: 0.9464 (mt) cc_final: 0.9064 (mt) REVERT: d 141 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7368 (ppp) REVERT: e 25 MET cc_start: 0.9136 (tpp) cc_final: 0.8926 (tpp) REVERT: e 31 GLU cc_start: 0.9082 (tt0) cc_final: 0.8766 (tm-30) REVERT: e 51 ASN cc_start: 0.9248 (m-40) cc_final: 0.8888 (p0) REVERT: e 95 MET cc_start: 0.7566 (ptm) cc_final: 0.7237 (ptm) REVERT: e 140 ILE cc_start: 0.5551 (mt) cc_final: 0.5193 (mp) REVERT: f 123 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7506 (tm-30) REVERT: g 7 ASP cc_start: 0.8103 (m-30) cc_final: 0.7659 (m-30) REVERT: i 129 GLU cc_start: 0.9029 (tt0) cc_final: 0.8740 (tm-30) REVERT: i 133 ARG cc_start: 0.6717 (ttm110) cc_final: 0.6240 (ttp-110) REVERT: j 57 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6170 (pp) REVERT: j 69 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7976 (ttm110) REVERT: j 76 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8032 (p-80) REVERT: j 91 GLU cc_start: 0.8740 (tt0) cc_final: 0.8458 (tp30) REVERT: j 98 GLU cc_start: 0.8555 (pm20) cc_final: 0.8236 (pm20) REVERT: j 140 LEU cc_start: 0.7680 (tp) cc_final: 0.7292 (tt) REVERT: k 12 ASP cc_start: 0.8509 (p0) cc_final: 0.8208 (p0) REVERT: k 17 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7876 (ttp80) REVERT: k 39 ILE cc_start: 0.8428 (pt) cc_final: 0.7384 (mm) REVERT: k 113 MET cc_start: 0.8275 (mmm) cc_final: 0.7983 (mmm) REVERT: k 121 GLU cc_start: 0.7296 (mp0) cc_final: 0.7058 (mp0) REVERT: l 10 GLU cc_start: 0.8812 (tp30) cc_final: 0.7901 (pp20) REVERT: l 41 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6040 (mmm-85) REVERT: l 54 GLN cc_start: 0.7747 (tt0) cc_final: 0.7543 (pp30) REVERT: l 55 MET cc_start: 0.8468 (mmt) cc_final: 0.8028 (tpp) REVERT: l 58 TYR cc_start: 0.8337 (p90) cc_final: 0.8115 (p90) REVERT: l 70 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8531 (tttt) REVERT: l 103 ILE cc_start: 0.8432 (mt) cc_final: 0.8220 (mt) REVERT: m 22 GLN cc_start: 0.1869 (OUTLIER) cc_final: 0.1349 (pt0) REVERT: m 68 PHE cc_start: 0.8085 (t80) cc_final: 0.7872 (t80) REVERT: m 117 PHE cc_start: 0.8880 (m-10) cc_final: 0.8524 (m-80) REVERT: n 4 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8481 (mmt180) REVERT: n 12 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7049 (ttt90) REVERT: n 24 MET cc_start: 0.8799 (ttp) cc_final: 0.8501 (ptm) REVERT: n 35 LYS cc_start: 0.7711 (tmtt) cc_final: 0.6928 (tmtt) REVERT: n 49 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8153 (mm-30) REVERT: n 112 TYR cc_start: 0.7551 (m-80) cc_final: 0.6746 (m-80) REVERT: o 18 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7965 (mm) REVERT: o 63 LYS cc_start: 0.8794 (tttm) cc_final: 0.8535 (tttp) REVERT: o 84 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: p 23 ASP cc_start: 0.7436 (t0) cc_final: 0.7168 (t0) REVERT: p 43 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: p 61 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7532 (ttt90) REVERT: p 71 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8096 (ttm170) REVERT: q 5 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7209 (ptt-90) REVERT: q 35 PHE cc_start: 0.8450 (t80) cc_final: 0.7472 (t80) REVERT: q 51 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8310 (tp40) REVERT: q 54 ARG cc_start: 0.7498 (mmt180) cc_final: 0.6989 (mmm160) REVERT: q 56 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.5982 (m-10) REVERT: r 23 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: r 37 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6550 (pm20) REVERT: r 86 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: s 29 VAL cc_start: 0.8479 (m) cc_final: 0.7897 (m) REVERT: s 48 LYS cc_start: 0.9014 (tttt) cc_final: 0.8587 (tttp) REVERT: s 68 ASP cc_start: 0.8659 (t0) cc_final: 0.8441 (t0) REVERT: s 69 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (mt) REVERT: t 48 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6912 (mm-40) REVERT: t 86 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7030 (t) REVERT: t 87 LEU cc_start: 0.8016 (tp) cc_final: 0.7597 (tp) REVERT: u 95 PHE cc_start: 0.6228 (m-10) cc_final: 0.5939 (m-10) REVERT: u 97 SER cc_start: 0.8573 (t) cc_final: 0.8051 (p) REVERT: v 2 PHE cc_start: 0.5589 (m-80) cc_final: 0.4732 (m-10) REVERT: v 11 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8468 (tm-30) REVERT: v 26 PHE cc_start: 0.7394 (p90) cc_final: 0.7094 (p90) REVERT: v 50 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6648 (ttp) REVERT: v 56 PHE cc_start: 0.7668 (t80) cc_final: 0.6707 (t80) REVERT: w 39 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8226 (m) REVERT: x 33 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.6393 (m-70) REVERT: y 5 GLU cc_start: 0.8021 (tp30) cc_final: 0.7766 (tp30) REVERT: y 26 PHE cc_start: 0.8678 (t80) cc_final: 0.8389 (t80) REVERT: y 30 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7414 (mmp) REVERT: B 16 ARG cc_start: 0.9233 (mtt180) cc_final: 0.8293 (mtt90) REVERT: D 19 ARG cc_start: 0.9045 (mtp180) cc_final: 0.8583 (ttp-170) REVERT: E 2 LYS cc_start: 0.8387 (mttt) cc_final: 0.8005 (mtpt) REVERT: E 43 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8528 (mm) REVERT: G 15 PHE cc_start: 0.9258 (m-80) cc_final: 0.8782 (m-80) REVERT: G 21 TYR cc_start: 0.8295 (m-80) cc_final: 0.7846 (m-80) REVERT: G 31 PHE cc_start: 0.8751 (t80) cc_final: 0.8439 (t80) REVERT: G 48 MET cc_start: 0.9468 (mpp) cc_final: 0.9208 (mpp) REVERT: G 77 GLU cc_start: 0.8472 (pp20) cc_final: 0.8109 (pp20) REVERT: G 80 LYS cc_start: 0.8556 (tmmt) cc_final: 0.8280 (tmmt) REVERT: G 103 TRP cc_start: 0.8850 (t-100) cc_final: 0.8435 (t-100) REVERT: G 173 LYS cc_start: 0.8930 (tttt) cc_final: 0.8632 (pttp) REVERT: G 207 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8450 (ptp90) REVERT: G 211 LEU cc_start: 0.9390 (tt) cc_final: 0.9179 (mt) REVERT: G 212 TYR cc_start: 0.8140 (m-10) cc_final: 0.7836 (m-10) REVERT: H 39 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8284 (ttt-90) REVERT: H 114 LEU cc_start: 0.7556 (mt) cc_final: 0.7263 (tt) REVERT: H 125 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8612 (mtm180) REVERT: H 137 VAL cc_start: 0.8138 (t) cc_final: 0.7619 (t) REVERT: H 138 GLN cc_start: 0.8983 (tp40) cc_final: 0.8782 (tm-30) REVERT: H 141 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.4821 (ptp) REVERT: H 146 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8132 (mmmt) REVERT: H 149 LYS cc_start: 0.8226 (tttm) cc_final: 0.7937 (tptp) REVERT: H 184 ASN cc_start: 0.7182 (t0) cc_final: 0.6442 (t0) REVERT: I 74 TYR cc_start: 0.7791 (m-80) cc_final: 0.7187 (m-80) REVERT: I 92 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8204 (mt) REVERT: I 162 GLU cc_start: 0.8849 (tp30) cc_final: 0.8577 (mp0) REVERT: I 171 GLU cc_start: 0.4764 (tp30) cc_final: 0.4009 (pm20) REVERT: I 195 ASN cc_start: 0.7686 (t0) cc_final: 0.7419 (t0) REVERT: J 25 LYS cc_start: 0.8252 (tptt) cc_final: 0.7720 (tptp) REVERT: J 68 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8907 (ttp80) REVERT: J 69 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8716 (m-40) REVERT: J 92 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7185 (mtm180) REVERT: J 110 MET cc_start: 0.8173 (mpp) cc_final: 0.7293 (mpp) REVERT: J 150 GLU cc_start: 0.8874 (tp30) cc_final: 0.8542 (tp30) REVERT: J 151 MET cc_start: 0.9336 (mmp) cc_final: 0.9029 (mmm) REVERT: K 86 ARG cc_start: 0.4679 (ttm170) cc_final: 0.4283 (mmt-90) REVERT: L 73 GLU cc_start: 0.9302 (pt0) cc_final: 0.8555 (pp20) REVERT: L 115 MET cc_start: 0.5859 (mmt) cc_final: 0.5630 (mmm) REVERT: M 14 ARG cc_start: 0.7568 (ttm110) cc_final: 0.6588 (mtp180) REVERT: M 49 LYS cc_start: 0.9025 (tttt) cc_final: 0.8654 (tttp) REVERT: M 61 THR cc_start: 0.8379 (m) cc_final: 0.8137 (p) REVERT: M 63 LYS cc_start: 0.7834 (mttp) cc_final: 0.7177 (mttm) REVERT: M 86 LYS cc_start: 0.8548 (mmtt) cc_final: 0.6896 (mmmt) REVERT: M 90 GLU cc_start: 0.8322 (tt0) cc_final: 0.7598 (tm-30) REVERT: N 45 MET cc_start: 0.6368 (mtm) cc_final: 0.5585 (mtm) REVERT: N 48 ARG cc_start: 0.6787 (ptt-90) cc_final: 0.5945 (ttm-80) REVERT: N 86 LEU cc_start: 0.6790 (mt) cc_final: 0.6505 (pp) REVERT: N 89 TYR cc_start: 0.5282 (m-80) cc_final: 0.4879 (m-80) REVERT: O 63 ASP cc_start: 0.8795 (m-30) cc_final: 0.8436 (m-30) REVERT: P 37 GLN cc_start: 0.8194 (tp40) cc_final: 0.7764 (tm-30) REVERT: P 39 ASN cc_start: 0.8227 (m110) cc_final: 0.7167 (m-40) REVERT: P 45 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6877 (t) REVERT: P 92 ARG cc_start: 0.6048 (ttp-170) cc_final: 0.5534 (tmm-80) REVERT: P 108 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8295 (p0) REVERT: Q 45 ASN cc_start: 0.7037 (m-40) cc_final: 0.6313 (m-40) REVERT: R 49 GLU cc_start: 0.7834 (tp30) cc_final: 0.7421 (tp30) REVERT: R 53 ASP cc_start: 0.8625 (p0) cc_final: 0.8378 (p0) REVERT: T 21 THR cc_start: 0.7179 (p) cc_final: 0.6781 (p) REVERT: T 34 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.5446 (mm-40) REVERT: T 42 PHE cc_start: 0.7118 (m-10) cc_final: 0.6858 (m-10) REVERT: T 58 MET cc_start: 0.8559 (tmm) cc_final: 0.8198 (tmm) REVERT: U 77 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8903 (mt-10) REVERT: V 15 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8365 (ptpp) REVERT: V 36 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6361 (t80) REVERT: V 46 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6145 (t70) REVERT: V 79 GLU cc_start: 0.3607 (OUTLIER) cc_final: 0.3399 (pm20) REVERT: W 47 ARG cc_start: 0.7297 (mpt90) cc_final: 0.6942 (mmm-85) REVERT: W 52 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8185 (ttm170) REVERT: W 59 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7576 (tptp) REVERT: W 60 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6314 (ptp-110) REVERT: X 31 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8052 (ttp-110) REVERT: Y 17 ARG cc_start: 0.9146 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: Y 18 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8913 (mmmt) REVERT: Y 69 ASN cc_start: 0.7401 (t0) cc_final: 0.7188 (t0) REVERT: Z 16 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8692 (mtp180) REVERT: Z 36 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6612 (m-10) outliers start: 422 outliers final: 263 residues processed: 1527 average time/residue: 1.4979 time to fit residues: 3900.1484 Evaluate side-chains 1515 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1212 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 57 HIS Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 259 ASN Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 125 SER Chi-restraints excluded: chain d residue 141 MET Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 98 PHE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 166 GLU Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 12 ARG Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 84 GLU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 47 ARG Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 64 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 23 GLU Chi-restraints excluded: chain r residue 37 GLU Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 61 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 50 MET Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain y residue 15 ASN Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 30 MET Chi-restraints excluded: chain y residue 53 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 70 HIS Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 15 LYS Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 79 GLU Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 9 PHE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 173 THR 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: 40.0000 chunk 14 optimal weight: 9.9990 chunk 760 optimal weight: 30.0000 chunk 421 optimal weight: 4.9990 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 521 optimal weight: 1.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 HIS ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 HIS g 11 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 GLN q 43 GLN q 55 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 38 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 163139 Z= 0.262 Angle : 0.729 11.949 244082 Z= 0.372 Chirality : 0.040 0.294 31220 Planarity : 0.005 0.084 13080 Dihedral : 24.196 178.968 81729 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 30.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.52 % Favored : 88.29 % Rotamer: Outliers : 6.93 % Allowed : 25.94 % Favored : 67.14 % 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: -3.16 (0.10), residues: 5919 helix: -1.16 (0.11), residues: 1806 sheet: -2.25 (0.16), residues: 907 loop : -2.68 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 43 HIS 0.018 0.002 HIS E 25 PHE 0.043 0.003 PHE o 92 TYR 0.019 0.002 TYR e 6 ARG 0.016 0.001 ARG V 64 *********************** 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 1626 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1286 time to evaluate : 6.319 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: b 47 ARG cc_start: 0.8414 (mtt180) cc_final: 0.6988 (mmt90) REVERT: b 186 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: b 193 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: b 263 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: c 40 LEU cc_start: 0.8111 (mp) cc_final: 0.7727 (mt) REVERT: c 79 LEU cc_start: 0.8944 (mt) cc_final: 0.8514 (mt) REVERT: c 127 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: c 188 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8297 (mm) REVERT: d 29 HIS cc_start: 0.8115 (t-90) cc_final: 0.7287 (t70) REVERT: d 61 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7770 (ptp90) REVERT: d 73 ILE cc_start: 0.8842 (tt) cc_final: 0.8252 (tt) REVERT: d 78 TRP cc_start: 0.8498 (m-10) cc_final: 0.8261 (m-10) REVERT: d 101 TYR cc_start: 0.8469 (t80) cc_final: 0.8028 (t80) REVERT: d 112 LEU cc_start: 0.9501 (mt) cc_final: 0.9134 (mt) REVERT: d 131 THR cc_start: 0.8922 (p) cc_final: 0.8702 (p) REVERT: d 171 ASP cc_start: 0.8378 (t70) cc_final: 0.7829 (t70) REVERT: e 31 GLU cc_start: 0.9030 (tt0) cc_final: 0.8702 (tm-30) REVERT: e 140 ILE cc_start: 0.5602 (mt) cc_final: 0.5265 (mp) REVERT: f 123 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7427 (tm-30) REVERT: g 7 ASP cc_start: 0.7983 (m-30) cc_final: 0.7601 (m-30) REVERT: i 133 ARG cc_start: 0.6603 (ttm110) cc_final: 0.6319 (ttp-110) REVERT: j 57 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6163 (pp) REVERT: j 69 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8162 (tpp-160) REVERT: j 76 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8016 (p-80) REVERT: j 91 GLU cc_start: 0.8479 (tt0) cc_final: 0.8155 (tp30) REVERT: j 140 LEU cc_start: 0.7628 (tp) cc_final: 0.7288 (tt) REVERT: k 7 MET cc_start: 0.8216 (tpp) cc_final: 0.7774 (tpt) REVERT: k 12 ASP cc_start: 0.8477 (p0) cc_final: 0.8148 (p0) REVERT: k 20 MET cc_start: 0.7144 (ptt) cc_final: 0.6491 (ptt) REVERT: k 40 LYS cc_start: 0.9340 (tppt) cc_final: 0.8852 (tptp) REVERT: k 64 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8345 (mtt180) REVERT: k 98 ARG cc_start: 0.7197 (mmt180) cc_final: 0.6560 (mmt180) REVERT: k 116 ILE cc_start: 0.8880 (pp) cc_final: 0.8268 (pp) REVERT: k 121 GLU cc_start: 0.7021 (mp0) cc_final: 0.6816 (mp0) REVERT: l 10 GLU cc_start: 0.8792 (tp30) cc_final: 0.7825 (pp20) REVERT: l 41 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.5951 (mmm-85) REVERT: l 55 MET cc_start: 0.8415 (mmt) cc_final: 0.8152 (tpp) REVERT: l 58 TYR cc_start: 0.8243 (p90) cc_final: 0.7920 (p90) REVERT: l 70 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8385 (tttt) REVERT: m 22 GLN cc_start: 0.0809 (OUTLIER) cc_final: 0.0385 (pt0) REVERT: m 53 MET cc_start: 0.8590 (tmm) cc_final: 0.8371 (tmm) REVERT: m 68 PHE cc_start: 0.7888 (t80) cc_final: 0.7525 (t80) REVERT: m 82 MET cc_start: 0.5250 (tpp) cc_final: 0.4862 (tpp) REVERT: m 117 PHE cc_start: 0.8809 (m-10) cc_final: 0.8550 (m-80) REVERT: n 4 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8449 (mmt180) REVERT: n 13 ASN cc_start: 0.8426 (p0) cc_final: 0.8116 (p0) REVERT: n 20 MET cc_start: 0.8345 (ppp) cc_final: 0.7770 (ppp) REVERT: n 24 MET cc_start: 0.8584 (ttp) cc_final: 0.8194 (ptm) REVERT: n 35 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7231 (tmtt) REVERT: n 49 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8000 (mm-30) REVERT: n 112 TYR cc_start: 0.7645 (m-80) cc_final: 0.7047 (m-80) REVERT: o 18 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7947 (mm) REVERT: o 63 LYS cc_start: 0.8787 (tttm) cc_final: 0.8516 (tttp) REVERT: o 84 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: p 23 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7274 (t0) REVERT: p 40 GLN cc_start: 0.4202 (OUTLIER) cc_final: 0.3774 (mp10) REVERT: p 43 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: p 61 ARG cc_start: 0.8051 (ttt90) cc_final: 0.7595 (ttt90) REVERT: q 5 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7167 (ptt-90) REVERT: q 51 GLN cc_start: 0.8473 (tp40) cc_final: 0.7972 (tp40) REVERT: q 56 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.5828 (m-10) REVERT: r 22 LEU cc_start: 0.8038 (pt) cc_final: 0.7410 (pp) REVERT: r 70 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (tp30) REVERT: r 79 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8566 (ptt180) REVERT: r 86 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: s 8 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7298 (mtm110) REVERT: s 48 LYS cc_start: 0.8967 (tttt) cc_final: 0.8538 (tttm) REVERT: s 69 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7629 (mt) REVERT: t 48 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7119 (mm-40) REVERT: u 95 PHE cc_start: 0.6195 (m-10) cc_final: 0.5878 (m-10) REVERT: u 97 SER cc_start: 0.8509 (t) cc_final: 0.8023 (p) REVERT: v 2 PHE cc_start: 0.5686 (m-80) cc_final: 0.4682 (m-10) REVERT: v 26 PHE cc_start: 0.7323 (p90) cc_final: 0.7091 (p90) REVERT: v 50 MET cc_start: 0.8220 (ttp) cc_final: 0.7508 (ttp) REVERT: v 56 PHE cc_start: 0.7695 (t80) cc_final: 0.6591 (t80) REVERT: v 87 GLN cc_start: 0.6909 (pm20) cc_final: 0.6508 (pp30) REVERT: w 39 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (m) REVERT: y 24 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: y 30 MET cc_start: 0.7631 (mmp) cc_final: 0.7264 (mmp) REVERT: B 16 ARG cc_start: 0.9253 (mtt180) cc_final: 0.8315 (mtt90) REVERT: C 19 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7591 (p90) REVERT: D 19 ARG cc_start: 0.9066 (mtp180) cc_final: 0.8564 (ttp-170) REVERT: E 2 LYS cc_start: 0.8293 (mttt) cc_final: 0.7987 (mtpt) REVERT: E 4 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8058 (mmmt) REVERT: E 40 LYS cc_start: 0.8134 (mttt) cc_final: 0.7843 (mttt) REVERT: E 43 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8442 (mm) REVERT: G 15 PHE cc_start: 0.9211 (m-80) cc_final: 0.8775 (m-80) REVERT: G 19 THR cc_start: 0.3057 (OUTLIER) cc_final: 0.2672 (p) REVERT: G 21 TYR cc_start: 0.8256 (m-80) cc_final: 0.7816 (m-80) REVERT: G 48 MET cc_start: 0.9448 (mpp) cc_final: 0.9027 (mpp) REVERT: G 77 GLU cc_start: 0.8429 (pp20) cc_final: 0.7923 (pp20) REVERT: G 80 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8215 (tmmt) REVERT: G 103 TRP cc_start: 0.8842 (t-100) cc_final: 0.8488 (t-100) REVERT: G 164 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.6148 (m-30) REVERT: G 173 LYS cc_start: 0.8567 (tttt) cc_final: 0.8334 (pttp) REVERT: G 207 ARG cc_start: 0.8997 (ptt-90) cc_final: 0.8425 (ptp90) REVERT: G 211 LEU cc_start: 0.9442 (tt) cc_final: 0.9190 (mt) REVERT: G 212 TYR cc_start: 0.8051 (m-10) cc_final: 0.7733 (m-10) REVERT: H 39 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7171 (mmm160) REVERT: H 114 LEU cc_start: 0.7493 (mt) cc_final: 0.7278 (tt) REVERT: H 133 MET cc_start: 0.7755 (mmm) cc_final: 0.7511 (mmt) REVERT: H 141 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6223 (tpp) REVERT: H 146 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7911 (mmmt) REVERT: H 169 GLU cc_start: 0.8555 (tp30) cc_final: 0.8102 (tm-30) REVERT: H 184 ASN cc_start: 0.7256 (t0) cc_final: 0.6535 (t0) REVERT: I 74 TYR cc_start: 0.7863 (m-80) cc_final: 0.7040 (m-80) REVERT: I 162 GLU cc_start: 0.8827 (tp30) cc_final: 0.8554 (mp0) REVERT: I 195 ASN cc_start: 0.7705 (t0) cc_final: 0.7447 (t0) REVERT: J 25 LYS cc_start: 0.8109 (tptt) cc_final: 0.7600 (tptp) REVERT: J 92 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7072 (mtm180) REVERT: J 110 MET cc_start: 0.8063 (mpp) cc_final: 0.7416 (mpp) REVERT: J 150 GLU cc_start: 0.8836 (tp30) cc_final: 0.8542 (tp30) REVERT: J 151 MET cc_start: 0.9281 (mmp) cc_final: 0.8966 (mmm) REVERT: K 46 GLN cc_start: 0.9221 (mt0) cc_final: 0.8624 (pp30) REVERT: K 49 TYR cc_start: 0.8278 (p90) cc_final: 0.7373 (p90) REVERT: L 73 GLU cc_start: 0.9210 (pt0) cc_final: 0.8541 (pp20) REVERT: L 89 GLU cc_start: 0.8020 (tp30) cc_final: 0.7647 (tp30) REVERT: M 14 ARG cc_start: 0.7336 (ttm110) cc_final: 0.6263 (mtp180) REVERT: M 49 LYS cc_start: 0.9033 (tttt) cc_final: 0.8690 (tttp) REVERT: M 61 THR cc_start: 0.8447 (m) cc_final: 0.8164 (p) REVERT: M 63 LYS cc_start: 0.8080 (mttp) cc_final: 0.7606 (mttm) REVERT: M 86 LYS cc_start: 0.8444 (mmtt) cc_final: 0.6974 (mmmt) REVERT: M 90 GLU cc_start: 0.8206 (tt0) cc_final: 0.7559 (tm-30) REVERT: M 91 LEU cc_start: 0.8711 (tp) cc_final: 0.8474 (pp) REVERT: N 45 MET cc_start: 0.6394 (mtm) cc_final: 0.5682 (mtm) REVERT: N 48 ARG cc_start: 0.6882 (ptt-90) cc_final: 0.6024 (ttm-80) REVERT: N 89 TYR cc_start: 0.5167 (m-80) cc_final: 0.4786 (m-80) REVERT: N 117 LEU cc_start: 0.8818 (mt) cc_final: 0.8567 (tp) REVERT: N 123 ARG cc_start: 0.8302 (mmt90) cc_final: 0.7987 (mmt90) REVERT: O 63 ASP cc_start: 0.8733 (m-30) cc_final: 0.8444 (m-30) REVERT: P 37 GLN cc_start: 0.8235 (tp40) cc_final: 0.7770 (tm-30) REVERT: P 39 ASN cc_start: 0.8273 (m110) cc_final: 0.7247 (m-40) REVERT: P 45 THR cc_start: 0.6793 (t) cc_final: 0.6586 (t) REVERT: Q 45 ASN cc_start: 0.6767 (m-40) cc_final: 0.6348 (m-40) REVERT: R 49 GLU cc_start: 0.7795 (tp30) cc_final: 0.7350 (tp30) REVERT: R 53 ASP cc_start: 0.8509 (p0) cc_final: 0.8266 (p0) REVERT: S 19 TYR cc_start: 0.7830 (m-80) cc_final: 0.7562 (m-80) REVERT: T 2 LEU cc_start: 0.8248 (mt) cc_final: 0.7943 (mt) REVERT: T 34 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5745 (mm-40) REVERT: T 63 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7306 (mmt90) REVERT: U 25 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7842 (mtt-85) REVERT: U 77 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8867 (mt-10) REVERT: V 36 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6143 (t80) REVERT: V 76 ARG cc_start: 0.6672 (ttp-110) cc_final: 0.6347 (tmm-80) REVERT: W 47 ARG cc_start: 0.7225 (mpt90) cc_final: 0.6984 (mmm-85) REVERT: W 52 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8194 (ttm170) REVERT: W 54 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7809 (tp) REVERT: W 59 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7497 (tptp) REVERT: W 60 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6436 (ptp-110) REVERT: X 31 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8111 (tmm-80) REVERT: Y 26 MET cc_start: 0.8449 (ttt) cc_final: 0.7729 (ttm) REVERT: Y 30 PHE cc_start: 0.8392 (m-10) cc_final: 0.7573 (m-80) REVERT: Y 33 LYS cc_start: 0.8230 (mttp) cc_final: 0.8002 (mptt) REVERT: Z 36 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: Z 37 TYR cc_start: 0.7328 (t80) cc_final: 0.6871 (t80) REVERT: Z 38 GLU cc_start: 0.8050 (tp30) cc_final: 0.7777 (tp30) REVERT: Z 54 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6729 (ttt180) outliers start: 340 outliers final: 226 residues processed: 1477 average time/residue: 1.3766 time to fit residues: 3436.9157 Evaluate side-chains 1459 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1203 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 193 GLU Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 166 GLU Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 17 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 84 GLU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 70 HIS Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 35 ILE Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 38 LYS Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 7.9990 chunk 920 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 599 optimal weight: 40.0000 chunk 252 optimal weight: 3.9990 chunk 1022 optimal weight: 20.0000 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 338 optimal weight: 0.9990 chunk 536 optimal weight: 8.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN m 13 HIS ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS N 3 ASN N 36 GLN ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 HIS P 100 ASN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN ** 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: 0.7477 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 163139 Z= 0.170 Angle : 0.627 16.144 244082 Z= 0.319 Chirality : 0.035 0.309 31220 Planarity : 0.005 0.081 13080 Dihedral : 23.934 178.465 81728 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.46 % Favored : 90.37 % Rotamer: Outliers : 5.56 % Allowed : 27.97 % Favored : 66.46 % 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: -2.86 (0.10), residues: 5919 helix: -0.87 (0.12), residues: 1817 sheet: -2.05 (0.16), residues: 932 loop : -2.52 (0.10), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 43 HIS 0.018 0.001 HIS Y 67 PHE 0.040 0.002 PHE l 50 TYR 0.020 0.001 TYR n 94 ARG 0.013 0.001 ARG V 64 *********************** 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 1597 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1324 time to evaluate : 6.383 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 47 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7414 (mmt90) REVERT: b 186 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: c 1 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5752 (ppp) REVERT: c 40 LEU cc_start: 0.8007 (mp) cc_final: 0.7529 (mt) REVERT: c 79 LEU cc_start: 0.8884 (mt) cc_final: 0.8550 (mt) REVERT: c 127 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: c 173 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: c 188 LEU cc_start: 0.8569 (mm) cc_final: 0.8244 (mm) REVERT: d 21 ARG cc_start: 0.8606 (ttm170) cc_final: 0.7896 (ttt180) REVERT: d 24 ASN cc_start: 0.6970 (m-40) cc_final: 0.6218 (m110) REVERT: d 29 HIS cc_start: 0.8108 (t-90) cc_final: 0.7280 (t-90) REVERT: d 61 ARG cc_start: 0.8064 (mpp-170) cc_final: 0.7639 (ptp90) REVERT: d 73 ILE cc_start: 0.8755 (tt) cc_final: 0.8205 (tt) REVERT: d 78 TRP cc_start: 0.8404 (m-10) cc_final: 0.8189 (m-10) REVERT: d 85 PHE cc_start: 0.7699 (m-80) cc_final: 0.7305 (m-80) REVERT: d 101 TYR cc_start: 0.8627 (t80) cc_final: 0.8343 (t80) REVERT: d 112 LEU cc_start: 0.9480 (mt) cc_final: 0.9120 (mt) REVERT: d 131 THR cc_start: 0.8660 (p) cc_final: 0.8422 (p) REVERT: d 188 MET cc_start: 0.8916 (mmp) cc_final: 0.8302 (mmp) REVERT: e 31 GLU cc_start: 0.8998 (tt0) cc_final: 0.8715 (tm-30) REVERT: e 51 ASN cc_start: 0.9310 (m-40) cc_final: 0.8906 (p0) REVERT: e 119 LYS cc_start: 0.9262 (tptp) cc_final: 0.8587 (mmmt) REVERT: e 140 ILE cc_start: 0.5532 (mt) cc_final: 0.5209 (mp) REVERT: f 103 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (p0) REVERT: f 123 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7220 (tm-30) REVERT: g 7 ASP cc_start: 0.8014 (m-30) cc_final: 0.7654 (m-30) REVERT: i 133 ARG cc_start: 0.6501 (ttm110) cc_final: 0.5600 (ttp80) REVERT: j 12 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8355 (tptp) REVERT: j 57 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6450 (pp) REVERT: j 76 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8181 (p-80) REVERT: j 92 MET cc_start: 0.8417 (tpt) cc_final: 0.7994 (tpp) REVERT: j 140 LEU cc_start: 0.7559 (tp) cc_final: 0.7260 (tt) REVERT: k 12 ASP cc_start: 0.8412 (p0) cc_final: 0.8073 (p0) REVERT: k 40 LYS cc_start: 0.9328 (tppt) cc_final: 0.8956 (tppt) REVERT: k 87 LEU cc_start: 0.6371 (tp) cc_final: 0.5924 (mt) REVERT: l 10 GLU cc_start: 0.8760 (tp30) cc_final: 0.7781 (pp20) REVERT: l 41 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.5918 (mmm-85) REVERT: l 55 MET cc_start: 0.8313 (mmt) cc_final: 0.8020 (tpp) REVERT: l 58 TYR cc_start: 0.8346 (p90) cc_final: 0.8025 (p90) REVERT: l 70 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8418 (tttt) REVERT: m 22 GLN cc_start: 0.0463 (OUTLIER) cc_final: 0.0245 (pt0) REVERT: m 53 MET cc_start: 0.8449 (tmm) cc_final: 0.8108 (tmm) REVERT: m 68 PHE cc_start: 0.7681 (t80) cc_final: 0.7189 (t80) REVERT: m 82 MET cc_start: 0.5689 (tpp) cc_final: 0.5306 (tpp) REVERT: n 12 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7329 (ttm-80) REVERT: n 20 MET cc_start: 0.8072 (ppp) cc_final: 0.7755 (ppp) REVERT: n 24 MET cc_start: 0.8548 (ttp) cc_final: 0.8232 (ptm) REVERT: n 49 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8303 (mm-30) REVERT: n 117 ASP cc_start: 0.8122 (t0) cc_final: 0.7517 (p0) REVERT: o 18 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7950 (mm) REVERT: o 62 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8468 (mt) REVERT: o 63 LYS cc_start: 0.8752 (tttm) cc_final: 0.8503 (tttp) REVERT: o 83 LEU cc_start: 0.8632 (mm) cc_final: 0.8413 (mm) REVERT: p 4 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8846 (mt) REVERT: p 23 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7371 (t0) REVERT: q 5 ARG cc_start: 0.7842 (ptt90) cc_final: 0.7583 (ptt-90) REVERT: q 51 GLN cc_start: 0.8154 (tp40) cc_final: 0.7935 (tp40) REVERT: q 54 ARG cc_start: 0.7373 (mmt180) cc_final: 0.7012 (mmp-170) REVERT: q 56 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.5706 (m-10) REVERT: r 13 ARG cc_start: 0.7687 (ptt90) cc_final: 0.7344 (tmm-80) REVERT: r 22 LEU cc_start: 0.7972 (pt) cc_final: 0.7390 (pp) REVERT: r 86 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: s 17 VAL cc_start: 0.8909 (t) cc_final: 0.8647 (t) REVERT: s 48 LYS cc_start: 0.8890 (tttt) cc_final: 0.8615 (tttt) REVERT: t 36 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8088 (mtmm) REVERT: t 68 LYS cc_start: 0.7322 (tttm) cc_final: 0.6387 (ttpt) REVERT: u 32 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7483 (mmmt) REVERT: u 95 PHE cc_start: 0.5928 (m-10) cc_final: 0.5508 (m-10) REVERT: u 97 SER cc_start: 0.8515 (t) cc_final: 0.8051 (p) REVERT: v 2 PHE cc_start: 0.5785 (m-10) cc_final: 0.5240 (m-80) REVERT: v 26 PHE cc_start: 0.7209 (p90) cc_final: 0.6851 (p90) REVERT: v 56 PHE cc_start: 0.7872 (t80) cc_final: 0.6693 (t80) REVERT: v 59 GLU cc_start: 0.7610 (tp30) cc_final: 0.7316 (tm-30) REVERT: v 87 GLN cc_start: 0.7047 (pm20) cc_final: 0.6738 (pp30) REVERT: w 39 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (m) REVERT: x 49 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7648 (mtp-110) REVERT: y 1 MET cc_start: 0.8757 (mtm) cc_final: 0.8132 (mtm) REVERT: y 13 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: B 16 ARG cc_start: 0.9258 (mtt180) cc_final: 0.8182 (mtt90) REVERT: E 2 LYS cc_start: 0.8190 (mttt) cc_final: 0.7803 (mtpt) REVERT: E 4 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7979 (mmmt) REVERT: E 15 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7198 (ttpt) REVERT: E 43 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8372 (mm) REVERT: F 12 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8260 (ttp80) REVERT: G 15 PHE cc_start: 0.9184 (m-80) cc_final: 0.8816 (m-80) REVERT: G 21 TYR cc_start: 0.8188 (m-80) cc_final: 0.7789 (m-80) REVERT: G 48 MET cc_start: 0.9455 (mpp) cc_final: 0.8982 (mpp) REVERT: G 77 GLU cc_start: 0.8384 (pp20) cc_final: 0.7846 (pp20) REVERT: G 80 LYS cc_start: 0.8493 (tmmt) cc_final: 0.8194 (tmmt) REVERT: G 164 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: G 207 ARG cc_start: 0.8964 (ptt-90) cc_final: 0.8367 (ptp90) REVERT: G 211 LEU cc_start: 0.9421 (tt) cc_final: 0.9169 (mt) REVERT: G 212 TYR cc_start: 0.7924 (m-10) cc_final: 0.7603 (m-10) REVERT: H 39 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7651 (mmm160) REVERT: H 55 VAL cc_start: 0.8431 (t) cc_final: 0.8082 (m) REVERT: H 129 PHE cc_start: 0.8106 (p90) cc_final: 0.7905 (p90) REVERT: H 146 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7926 (mmmt) REVERT: H 169 GLU cc_start: 0.8479 (tp30) cc_final: 0.8139 (tm-30) REVERT: H 184 ASN cc_start: 0.7248 (t0) cc_final: 0.6635 (t0) REVERT: I 69 ARG cc_start: 0.8368 (tmm160) cc_final: 0.7609 (tmt-80) REVERT: I 72 ARG cc_start: 0.8678 (tmm-80) cc_final: 0.8018 (tmm-80) REVERT: I 74 TYR cc_start: 0.7616 (m-80) cc_final: 0.7059 (m-80) REVERT: I 195 ASN cc_start: 0.7615 (t0) cc_final: 0.7310 (t0) REVERT: J 25 LYS cc_start: 0.7972 (tptt) cc_final: 0.7734 (tptp) REVERT: J 92 ARG cc_start: 0.7433 (mtm180) cc_final: 0.7094 (mtm180) REVERT: J 110 MET cc_start: 0.8002 (mpp) cc_final: 0.7536 (mpp) REVERT: J 150 GLU cc_start: 0.8751 (tp30) cc_final: 0.8483 (tp30) REVERT: K 9 MET cc_start: 0.8505 (mpp) cc_final: 0.8249 (mmp) REVERT: K 49 TYR cc_start: 0.8046 (p90) cc_final: 0.7274 (p90) REVERT: L 25 PHE cc_start: 0.8729 (m-80) cc_final: 0.8360 (m-80) REVERT: L 55 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8484 (ptpp) REVERT: L 73 GLU cc_start: 0.9167 (pt0) cc_final: 0.8497 (pp20) REVERT: L 89 GLU cc_start: 0.8007 (tp30) cc_final: 0.7601 (tp30) REVERT: L 100 MET cc_start: 0.8902 (mpp) cc_final: 0.8263 (mpp) REVERT: M 14 ARG cc_start: 0.7141 (ttm110) cc_final: 0.5999 (mtp180) REVERT: M 45 ILE cc_start: 0.8087 (mt) cc_final: 0.7708 (mt) REVERT: M 61 THR cc_start: 0.8070 (m) cc_final: 0.7608 (p) REVERT: M 63 LYS cc_start: 0.7961 (mttp) cc_final: 0.7265 (mttm) REVERT: M 86 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7105 (mmmt) REVERT: M 90 GLU cc_start: 0.8092 (tt0) cc_final: 0.7614 (tm-30) REVERT: M 91 LEU cc_start: 0.8871 (tp) cc_final: 0.8611 (pp) REVERT: N 11 ARG cc_start: 0.6953 (tmt170) cc_final: 0.6735 (tmt170) REVERT: N 48 ARG cc_start: 0.6673 (ptt-90) cc_final: 0.5973 (ttm-80) REVERT: N 49 GLN cc_start: 0.8412 (tt0) cc_final: 0.8150 (tt0) REVERT: N 89 TYR cc_start: 0.5068 (m-80) cc_final: 0.4686 (m-80) REVERT: N 117 LEU cc_start: 0.8809 (mt) cc_final: 0.8498 (mt) REVERT: N 123 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7873 (mmt90) REVERT: O 63 ASP cc_start: 0.8865 (m-30) cc_final: 0.8391 (m-30) REVERT: P 32 THR cc_start: 0.8757 (m) cc_final: 0.8409 (t) REVERT: P 39 ASN cc_start: 0.8211 (m110) cc_final: 0.7876 (m110) REVERT: P 45 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6526 (t) REVERT: Q 4 ASN cc_start: 0.7606 (t0) cc_final: 0.7283 (t0) REVERT: Q 45 ASN cc_start: 0.6483 (m-40) cc_final: 0.6222 (m-40) REVERT: Q 74 GLN cc_start: 0.7815 (pm20) cc_final: 0.7499 (pm20) REVERT: Q 116 TYR cc_start: 0.7979 (m-80) cc_final: 0.7772 (m-10) REVERT: R 49 GLU cc_start: 0.7839 (tp30) cc_final: 0.7488 (tp30) REVERT: R 53 ASP cc_start: 0.8452 (p0) cc_final: 0.8222 (p0) REVERT: T 36 ASN cc_start: 0.7578 (m110) cc_final: 0.7150 (m-40) REVERT: U 25 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7752 (mtt-85) REVERT: U 35 ARG cc_start: 0.7430 (ptm160) cc_final: 0.7026 (ptm-80) REVERT: U 77 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8940 (mt-10) REVERT: V 36 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6122 (t80) REVERT: V 57 VAL cc_start: 0.7358 (t) cc_final: 0.6915 (p) REVERT: W 23 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8040 (ptmt) REVERT: W 47 ARG cc_start: 0.7090 (mpt90) cc_final: 0.6745 (mmm-85) REVERT: W 52 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8348 (ttm170) REVERT: W 59 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7355 (tptp) REVERT: X 31 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.7780 (tmm-80) REVERT: X 65 MET cc_start: 0.7878 (ppp) cc_final: 0.7669 (ppp) REVERT: Y 20 ASN cc_start: 0.8271 (p0) cc_final: 0.7547 (p0) REVERT: Z 15 LEU cc_start: 0.9416 (tt) cc_final: 0.8941 (mp) REVERT: Z 36 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: Z 37 TYR cc_start: 0.7319 (t80) cc_final: 0.6813 (t80) REVERT: Z 38 GLU cc_start: 0.8204 (tp30) cc_final: 0.7959 (tp30) REVERT: a 210 LYS cc_start: 0.5857 (mmtt) cc_final: 0.5609 (mmmt) outliers start: 273 outliers final: 186 residues processed: 1477 average time/residue: 1.3797 time to fit residues: 3438.2818 Evaluate side-chains 1440 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1231 time to evaluate : 6.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 166 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 35 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain j residue 109 LEU Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 110 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 17 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 91 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 50 VAL Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain X residue 9 PHE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Z residue 12 ASP Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE 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: 4.9990 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 20.0000 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 621 optimal weight: 20.0000 chunk 470 optimal weight: 5.9990 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN g 43 ASN ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 13 HIS q 51 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 163139 Z= 0.357 Angle : 0.824 14.246 244082 Z= 0.413 Chirality : 0.043 0.320 31220 Planarity : 0.006 0.071 13080 Dihedral : 24.323 179.986 81728 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 36.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.45 % Favored : 87.36 % Rotamer: Outliers : 6.85 % Allowed : 28.87 % Favored : 64.28 % 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: -3.10 (0.10), residues: 5919 helix: -1.11 (0.11), residues: 1811 sheet: -2.17 (0.16), residues: 900 loop : -2.65 (0.10), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 43 HIS 0.024 0.002 HIS B 18 PHE 0.047 0.003 PHE l 50 TYR 0.024 0.003 TYR n 112 ARG 0.013 0.001 ARG V 64 *********************** 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 1591 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1255 time to evaluate : 6.277 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: b 47 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8068 (mtt180) REVERT: b 57 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: b 186 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: b 237 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7432 (ptp-170) REVERT: b 263 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: c 40 LEU cc_start: 0.8130 (mp) cc_final: 0.7701 (mt) REVERT: c 127 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: c 173 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: c 188 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8340 (mm) REVERT: d 29 HIS cc_start: 0.8154 (t-90) cc_final: 0.7380 (t-90) REVERT: d 61 ARG cc_start: 0.7930 (mpp-170) cc_final: 0.7450 (ptp90) REVERT: d 73 ILE cc_start: 0.8892 (tt) cc_final: 0.8250 (tt) REVERT: d 78 TRP cc_start: 0.8471 (m-10) cc_final: 0.8200 (m-10) REVERT: d 88 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7255 (mpt-90) REVERT: d 112 LEU cc_start: 0.9527 (mt) cc_final: 0.9175 (mt) REVERT: d 159 LEU cc_start: 0.7473 (mp) cc_final: 0.7062 (tp) REVERT: e 31 GLU cc_start: 0.9082 (tt0) cc_final: 0.8747 (tm-30) REVERT: e 51 ASN cc_start: 0.9256 (m-40) cc_final: 0.8950 (p0) REVERT: e 98 PHE cc_start: 0.3771 (OUTLIER) cc_final: 0.3328 (m-10) REVERT: e 140 ILE cc_start: 0.5463 (mt) cc_final: 0.5124 (mp) REVERT: g 7 ASP cc_start: 0.8117 (m-30) cc_final: 0.7727 (m-30) REVERT: i 135 MET cc_start: 0.5999 (mtp) cc_final: 0.5611 (mmt) REVERT: j 40 HIS cc_start: 0.8224 (p-80) cc_final: 0.7665 (p-80) REVERT: j 57 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6033 (pp) REVERT: j 69 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7806 (tpp-160) REVERT: j 76 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8432 (p-80) REVERT: j 91 GLU cc_start: 0.8577 (tt0) cc_final: 0.8264 (tp30) REVERT: j 140 LEU cc_start: 0.7679 (tp) cc_final: 0.7423 (tt) REVERT: k 12 ASP cc_start: 0.8514 (p0) cc_final: 0.8231 (p0) REVERT: k 39 ILE cc_start: 0.8009 (pt) cc_final: 0.6914 (mm) REVERT: k 64 ARG cc_start: 0.8696 (mtt90) cc_final: 0.8113 (mtt90) REVERT: k 116 ILE cc_start: 0.8843 (pp) cc_final: 0.8643 (pp) REVERT: l 3 LEU cc_start: 0.8210 (mp) cc_final: 0.7949 (mp) REVERT: l 10 GLU cc_start: 0.8803 (tp30) cc_final: 0.8229 (pt0) REVERT: l 55 MET cc_start: 0.8524 (mmt) cc_final: 0.8210 (tpp) REVERT: l 58 TYR cc_start: 0.8136 (p90) cc_final: 0.7686 (p90) REVERT: l 70 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8584 (tttt) REVERT: l 78 ARG cc_start: 0.8495 (mmt180) cc_final: 0.8059 (mtt90) REVERT: m 22 GLN cc_start: 0.1625 (OUTLIER) cc_final: 0.0640 (pt0) REVERT: m 68 PHE cc_start: 0.7795 (t80) cc_final: 0.7420 (t80) REVERT: m 117 PHE cc_start: 0.8763 (m-10) cc_final: 0.8543 (m-80) REVERT: n 13 ASN cc_start: 0.8485 (p0) cc_final: 0.8137 (p0) REVERT: n 17 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (ptm160) REVERT: n 24 MET cc_start: 0.8825 (ttp) cc_final: 0.8405 (ptm) REVERT: n 35 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7432 (tmtt) REVERT: n 49 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8306 (mm-30) REVERT: n 112 TYR cc_start: 0.7615 (m-80) cc_final: 0.7136 (m-80) REVERT: o 18 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7902 (mm) REVERT: p 23 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7213 (t70) REVERT: p 43 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7256 (pp20) REVERT: p 61 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7652 (ttt90) REVERT: q 5 ARG cc_start: 0.7848 (ptt90) cc_final: 0.7324 (ptt-90) REVERT: q 51 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7996 (tp40) REVERT: q 56 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.6016 (m-10) REVERT: r 22 LEU cc_start: 0.7823 (pt) cc_final: 0.7456 (pp) REVERT: r 23 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: r 79 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8508 (ptt180) REVERT: r 86 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: r 95 ASP cc_start: 0.7030 (m-30) cc_final: 0.6344 (t0) REVERT: s 48 LYS cc_start: 0.8958 (tttt) cc_final: 0.8505 (tttm) REVERT: s 69 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7540 (mt) REVERT: u 86 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5600 (t80) REVERT: u 97 SER cc_start: 0.8539 (t) cc_final: 0.8058 (p) REVERT: v 2 PHE cc_start: 0.5734 (m-10) cc_final: 0.4813 (m-10) REVERT: v 21 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7863 (ptp90) REVERT: v 26 PHE cc_start: 0.7533 (p90) cc_final: 0.7065 (p90) REVERT: v 50 MET cc_start: 0.8246 (ttp) cc_final: 0.7459 (ttp) REVERT: v 56 PHE cc_start: 0.7720 (t80) cc_final: 0.6858 (t80) REVERT: x 33 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.6640 (m-70) REVERT: y 5 GLU cc_start: 0.7606 (tp30) cc_final: 0.7376 (tp30) REVERT: y 12 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7006 (tm-30) REVERT: y 17 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: y 24 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: y 30 MET cc_start: 0.7762 (mmp) cc_final: 0.7425 (mmp) REVERT: z 44 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8225 (mmm160) REVERT: C 19 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7570 (p90) REVERT: E 2 LYS cc_start: 0.8393 (mttt) cc_final: 0.8022 (mtpt) REVERT: E 43 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8390 (mm) REVERT: G 15 PHE cc_start: 0.9170 (m-80) cc_final: 0.8772 (m-80) REVERT: G 19 THR cc_start: 0.2649 (OUTLIER) cc_final: 0.2272 (p) REVERT: G 21 TYR cc_start: 0.8297 (m-80) cc_final: 0.7882 (m-80) REVERT: G 48 MET cc_start: 0.9424 (mpp) cc_final: 0.8940 (mpp) REVERT: G 77 GLU cc_start: 0.8490 (pp20) cc_final: 0.8108 (pp20) REVERT: G 80 LYS cc_start: 0.8569 (tmmt) cc_final: 0.8272 (tmmt) REVERT: G 164 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.6078 (m-30) REVERT: G 207 ARG cc_start: 0.9069 (ptt-90) cc_final: 0.8454 (ptp90) REVERT: G 211 LEU cc_start: 0.9448 (tt) cc_final: 0.9199 (mt) REVERT: G 212 TYR cc_start: 0.8095 (m-10) cc_final: 0.7772 (m-10) REVERT: H 39 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7841 (mmm160) REVERT: H 55 VAL cc_start: 0.8555 (t) cc_final: 0.8208 (m) REVERT: H 138 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8618 (tm-30) REVERT: H 141 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5396 (ptt) REVERT: H 146 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7840 (mmmt) REVERT: H 169 GLU cc_start: 0.8503 (tp30) cc_final: 0.7957 (tm-30) REVERT: H 184 ASN cc_start: 0.7122 (t0) cc_final: 0.6390 (t0) REVERT: I 61 ARG cc_start: 0.7924 (mtp85) cc_final: 0.5683 (mtp85) REVERT: I 74 TYR cc_start: 0.7956 (m-80) cc_final: 0.7143 (m-80) REVERT: I 87 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6913 (pp20) REVERT: I 162 GLU cc_start: 0.8826 (tp30) cc_final: 0.8564 (mp0) REVERT: I 195 ASN cc_start: 0.7619 (t0) cc_final: 0.7337 (t0) REVERT: J 25 LYS cc_start: 0.8132 (tptt) cc_final: 0.7843 (tptp) REVERT: J 49 TYR cc_start: 0.7867 (t80) cc_final: 0.7640 (t80) REVERT: J 92 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7034 (mtm180) REVERT: J 110 MET cc_start: 0.8088 (mpp) cc_final: 0.7378 (mpp) REVERT: L 25 PHE cc_start: 0.8783 (m-80) cc_final: 0.8328 (m-80) REVERT: L 55 LYS cc_start: 0.8779 (ptpt) cc_final: 0.8566 (ptpp) REVERT: L 73 GLU cc_start: 0.9247 (pt0) cc_final: 0.8547 (pp20) REVERT: L 89 GLU cc_start: 0.8196 (tp30) cc_final: 0.7855 (tp30) REVERT: L 100 MET cc_start: 0.8829 (mpp) cc_final: 0.8075 (mpp) REVERT: M 14 ARG cc_start: 0.7362 (ttm110) cc_final: 0.6323 (mtp180) REVERT: M 61 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7711 (p) REVERT: M 63 LYS cc_start: 0.8015 (mttp) cc_final: 0.7401 (mttm) REVERT: M 86 LYS cc_start: 0.8561 (mmtt) cc_final: 0.6998 (mmmt) REVERT: M 90 GLU cc_start: 0.8357 (tt0) cc_final: 0.7672 (tm-30) REVERT: M 91 LEU cc_start: 0.8809 (tp) cc_final: 0.8601 (pp) REVERT: N 48 ARG cc_start: 0.6793 (ptt-90) cc_final: 0.6163 (ttm-80) REVERT: N 89 TYR cc_start: 0.5167 (m-80) cc_final: 0.4749 (m-80) REVERT: O 63 ASP cc_start: 0.8823 (m-30) cc_final: 0.8541 (m-30) REVERT: P 37 GLN cc_start: 0.8315 (tp40) cc_final: 0.7818 (tm-30) REVERT: P 39 ASN cc_start: 0.8296 (m110) cc_final: 0.7281 (m-40) REVERT: Q 4 ASN cc_start: 0.7807 (t0) cc_final: 0.7442 (t0) REVERT: Q 45 ASN cc_start: 0.6768 (m-40) cc_final: 0.6423 (m-40) REVERT: R 49 GLU cc_start: 0.7705 (tp30) cc_final: 0.7239 (tp30) REVERT: R 53 ASP cc_start: 0.8696 (p0) cc_final: 0.8415 (p0) REVERT: T 36 ASN cc_start: 0.7615 (m110) cc_final: 0.7077 (m-40) REVERT: U 25 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7878 (mtp85) REVERT: U 77 GLU cc_start: 0.9362 (mt-10) cc_final: 0.8935 (mt-10) REVERT: V 36 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6111 (t80) REVERT: V 59 GLU cc_start: 0.8286 (mp0) cc_final: 0.7274 (mp0) REVERT: W 47 ARG cc_start: 0.7283 (mpt90) cc_final: 0.6934 (mmm-85) REVERT: W 52 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8186 (ttm170) REVERT: W 54 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7847 (tp) REVERT: W 59 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7498 (tptp) REVERT: W 60 ARG cc_start: 0.7531 (ttm110) cc_final: 0.6797 (ptp-110) REVERT: X 31 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8055 (tmm-80) REVERT: Y 33 LYS cc_start: 0.8204 (mttp) cc_final: 0.7854 (mptt) REVERT: Y 73 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7443 (ttp-170) REVERT: Z 36 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: Z 37 TYR cc_start: 0.7470 (t80) cc_final: 0.6937 (t80) REVERT: Z 38 GLU cc_start: 0.8196 (tp30) cc_final: 0.7625 (tp30) REVERT: a 218 MET cc_start: 0.4138 (ttt) cc_final: 0.3101 (ttm) outliers start: 336 outliers final: 243 residues processed: 1447 average time/residue: 1.4615 time to fit residues: 3589.9085 Evaluate side-chains 1477 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1196 time to evaluate : 6.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 57 HIS Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 98 PHE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 17 ARG Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 112 ARG Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 91 ARG Chi-restraints excluded: chain r residue 23 GLU Chi-restraints excluded: chain r residue 35 PHE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 34 GLN Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 36 PHE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 20.0000 chunk 406 optimal weight: 30.0000 chunk 608 optimal weight: 10.0000 chunk 306 optimal weight: 0.0060 chunk 200 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 647 optimal weight: 20.0000 chunk 694 optimal weight: 30.0000 chunk 503 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 800 optimal weight: 10.0000 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 73 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 163139 Z= 0.295 Angle : 0.761 13.225 244082 Z= 0.385 Chirality : 0.041 0.327 31220 Planarity : 0.006 0.072 13080 Dihedral : 24.333 178.870 81728 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 32.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.89 % Favored : 87.94 % Rotamer: Outliers : 6.58 % Allowed : 29.38 % Favored : 64.04 % 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: -3.08 (0.10), residues: 5919 helix: -1.10 (0.11), residues: 1809 sheet: -2.20 (0.16), residues: 896 loop : -2.63 (0.10), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 103 HIS 0.026 0.002 HIS E 25 PHE 0.046 0.003 PHE l 50 TYR 0.020 0.002 TYR j 16 ARG 0.014 0.001 ARG f 162 *********************** 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 1569 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1246 time to evaluate : 6.270 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: b 47 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7989 (mtt180) REVERT: b 57 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7111 (t-90) REVERT: b 163 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (mm) REVERT: b 186 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: b 224 MET cc_start: 0.8614 (mmt) cc_final: 0.8233 (mmp) REVERT: b 228 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.5820 (m-30) REVERT: c 1 MET cc_start: 0.6437 (ppp) cc_final: 0.5896 (ppp) REVERT: c 40 LEU cc_start: 0.8162 (mp) cc_final: 0.7739 (mt) REVERT: c 127 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: c 173 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: c 188 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8236 (mm) REVERT: d 29 HIS cc_start: 0.8159 (t-90) cc_final: 0.7381 (t-90) REVERT: d 61 ARG cc_start: 0.7911 (mpp-170) cc_final: 0.7383 (ptp90) REVERT: d 73 ILE cc_start: 0.8851 (tt) cc_final: 0.8221 (tt) REVERT: d 78 TRP cc_start: 0.8485 (m-10) cc_final: 0.8216 (m-10) REVERT: d 88 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7166 (mpt-90) REVERT: d 112 LEU cc_start: 0.9526 (mt) cc_final: 0.9180 (mt) REVERT: d 159 LEU cc_start: 0.7493 (mp) cc_final: 0.7176 (tp) REVERT: e 31 GLU cc_start: 0.9064 (tt0) cc_final: 0.8696 (tm-30) REVERT: e 51 ASN cc_start: 0.9224 (m-40) cc_final: 0.8982 (p0) REVERT: e 129 MET cc_start: 0.7671 (ppp) cc_final: 0.7310 (ppp) REVERT: e 140 ILE cc_start: 0.6260 (mt) cc_final: 0.5923 (mp) REVERT: f 103 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8047 (p0) REVERT: f 162 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7811 (mtm110) REVERT: g 7 ASP cc_start: 0.8111 (m-30) cc_final: 0.7721 (m-30) REVERT: g 90 LEU cc_start: 0.4378 (pp) cc_final: 0.4007 (pp) REVERT: j 40 HIS cc_start: 0.8293 (p-80) cc_final: 0.7807 (p-80) REVERT: j 57 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6029 (pp) REVERT: j 69 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.7939 (tpp-160) REVERT: j 76 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8366 (p-80) REVERT: j 91 GLU cc_start: 0.8504 (tt0) cc_final: 0.8177 (tp30) REVERT: j 116 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6866 (ttt180) REVERT: j 140 LEU cc_start: 0.7424 (tp) cc_final: 0.7192 (tt) REVERT: k 7 MET cc_start: 0.8213 (tpp) cc_final: 0.7832 (tpt) REVERT: k 12 ASP cc_start: 0.8552 (p0) cc_final: 0.8205 (p0) REVERT: k 40 LYS cc_start: 0.9336 (tppt) cc_final: 0.8941 (tptp) REVERT: k 59 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8638 (mmtp) REVERT: k 64 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8124 (mtt90) REVERT: k 108 ARG cc_start: 0.7292 (tpm170) cc_final: 0.7003 (mmm160) REVERT: l 3 LEU cc_start: 0.8073 (mp) cc_final: 0.7846 (mp) REVERT: l 10 GLU cc_start: 0.8793 (tp30) cc_final: 0.7894 (pp20) REVERT: l 41 ARG cc_start: 0.7075 (mmm-85) cc_final: 0.5884 (mmm-85) REVERT: l 55 MET cc_start: 0.8535 (mmt) cc_final: 0.8316 (tpp) REVERT: l 58 TYR cc_start: 0.8252 (p90) cc_final: 0.7823 (p90) REVERT: l 78 ARG cc_start: 0.8506 (mmt180) cc_final: 0.7950 (mtm-85) REVERT: m 22 GLN cc_start: 0.1366 (OUTLIER) cc_final: 0.0147 (pt0) REVERT: m 68 PHE cc_start: 0.7709 (t80) cc_final: 0.7306 (t80) REVERT: m 117 PHE cc_start: 0.8825 (m-10) cc_final: 0.8519 (m-80) REVERT: n 13 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8211 (p0) REVERT: n 24 MET cc_start: 0.8801 (ttp) cc_final: 0.8404 (ptm) REVERT: n 49 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8518 (mm-30) REVERT: n 112 TYR cc_start: 0.7569 (m-80) cc_final: 0.7115 (m-80) REVERT: o 18 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7972 (mm) REVERT: p 23 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7222 (t70) REVERT: p 61 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7637 (ttt90) REVERT: q 5 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7164 (ptt-90) REVERT: q 13 HIS cc_start: 0.6806 (m170) cc_final: 0.6134 (m170) REVERT: q 56 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.5866 (m-10) REVERT: r 13 ARG cc_start: 0.7935 (ptt90) cc_final: 0.7598 (tmm-80) REVERT: r 23 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: r 79 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8572 (ptt180) REVERT: r 86 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: s 48 LYS cc_start: 0.8952 (tttt) cc_final: 0.8498 (tttm) REVERT: s 69 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7518 (mt) REVERT: u 86 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.5570 (t80) REVERT: u 97 SER cc_start: 0.8501 (t) cc_final: 0.8023 (p) REVERT: v 2 PHE cc_start: 0.5912 (m-10) cc_final: 0.5571 (m-10) REVERT: v 26 PHE cc_start: 0.7480 (p90) cc_final: 0.7056 (p90) REVERT: v 50 MET cc_start: 0.8267 (ttp) cc_final: 0.7977 (ttp) REVERT: x 33 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.6497 (m-70) REVERT: y 17 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6145 (tt0) REVERT: y 24 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7636 (mm-30) REVERT: y 25 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8465 (tm-30) REVERT: y 30 MET cc_start: 0.7770 (mmp) cc_final: 0.7376 (mmp) REVERT: z 44 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8278 (mmm160) REVERT: B 16 ARG cc_start: 0.9244 (mtt180) cc_final: 0.8195 (mtt90) REVERT: D 19 ARG cc_start: 0.8965 (mtp180) cc_final: 0.8490 (ttp-170) REVERT: E 2 LYS cc_start: 0.8339 (mttt) cc_final: 0.7971 (mtpt) REVERT: E 15 LYS cc_start: 0.7749 (ttpt) cc_final: 0.7325 (ttpt) REVERT: E 43 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8372 (mm) REVERT: G 15 PHE cc_start: 0.9151 (m-80) cc_final: 0.8746 (m-80) REVERT: G 19 THR cc_start: 0.2768 (OUTLIER) cc_final: 0.2464 (p) REVERT: G 21 TYR cc_start: 0.8313 (m-80) cc_final: 0.7835 (m-80) REVERT: G 77 GLU cc_start: 0.8496 (pp20) cc_final: 0.8104 (pp20) REVERT: G 80 LYS cc_start: 0.8564 (tmmt) cc_final: 0.8268 (tmmt) REVERT: G 164 ASP cc_start: 0.6369 (OUTLIER) cc_final: 0.6088 (m-30) REVERT: G 207 ARG cc_start: 0.9042 (ptt-90) cc_final: 0.8421 (ptp90) REVERT: G 211 LEU cc_start: 0.9444 (tt) cc_final: 0.9201 (mt) REVERT: G 212 TYR cc_start: 0.8094 (m-10) cc_final: 0.7767 (m-10) REVERT: H 39 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7806 (mmm160) REVERT: H 55 VAL cc_start: 0.8530 (t) cc_final: 0.8177 (m) REVERT: H 138 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: H 146 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7762 (mmmt) REVERT: H 169 GLU cc_start: 0.8534 (tp30) cc_final: 0.8166 (tm-30) REVERT: H 184 ASN cc_start: 0.7207 (t0) cc_final: 0.6482 (t0) REVERT: I 69 ARG cc_start: 0.8581 (tmt-80) cc_final: 0.8357 (tmt170) REVERT: I 72 ARG cc_start: 0.8763 (tmm-80) cc_final: 0.8354 (tmm-80) REVERT: I 74 TYR cc_start: 0.7901 (m-80) cc_final: 0.7084 (m-80) REVERT: I 87 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: I 162 GLU cc_start: 0.8838 (tp30) cc_final: 0.8575 (mp0) REVERT: I 195 ASN cc_start: 0.7576 (t0) cc_final: 0.7296 (t0) REVERT: J 25 LYS cc_start: 0.8077 (tptt) cc_final: 0.7773 (tptp) REVERT: J 49 TYR cc_start: 0.7911 (t80) cc_final: 0.7687 (t80) REVERT: J 92 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7015 (mtm180) REVERT: J 110 MET cc_start: 0.8051 (mpp) cc_final: 0.7425 (mpp) REVERT: J 133 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5570 (tp) REVERT: L 25 PHE cc_start: 0.8734 (m-80) cc_final: 0.8302 (m-80) REVERT: L 73 GLU cc_start: 0.9243 (pt0) cc_final: 0.8536 (pp20) REVERT: L 85 GLN cc_start: 0.8764 (pm20) cc_final: 0.8535 (pm20) REVERT: L 89 GLU cc_start: 0.8183 (tp30) cc_final: 0.7853 (tp30) REVERT: M 14 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6306 (mtp180) REVERT: M 61 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7651 (p) REVERT: M 63 LYS cc_start: 0.8039 (mttp) cc_final: 0.7391 (mttm) REVERT: M 86 LYS cc_start: 0.8495 (mmtt) cc_final: 0.6898 (mmmt) REVERT: M 90 GLU cc_start: 0.8263 (tt0) cc_final: 0.7664 (tm-30) REVERT: M 91 LEU cc_start: 0.8772 (tp) cc_final: 0.8558 (pp) REVERT: N 48 ARG cc_start: 0.6806 (ptt-90) cc_final: 0.6193 (ttm-80) REVERT: N 89 TYR cc_start: 0.5415 (m-80) cc_final: 0.4956 (m-80) REVERT: N 117 LEU cc_start: 0.9141 (mt) cc_final: 0.8850 (tp) REVERT: N 123 ARG cc_start: 0.8279 (mmt90) cc_final: 0.7921 (mmt90) REVERT: O 5 ARG cc_start: 0.7928 (tpp80) cc_final: 0.7701 (ttm110) REVERT: O 63 ASP cc_start: 0.8803 (m-30) cc_final: 0.8519 (m-30) REVERT: O 88 MET cc_start: 0.8901 (pmm) cc_final: 0.8615 (pmm) REVERT: P 37 GLN cc_start: 0.8398 (tp40) cc_final: 0.7907 (tm-30) REVERT: P 39 ASN cc_start: 0.8303 (m110) cc_final: 0.7265 (m-40) REVERT: Q 4 ASN cc_start: 0.7828 (t0) cc_final: 0.7469 (t0) REVERT: Q 45 ASN cc_start: 0.6595 (m-40) cc_final: 0.6273 (m-40) REVERT: R 49 GLU cc_start: 0.7833 (tp30) cc_final: 0.7387 (tp30) REVERT: R 53 ASP cc_start: 0.8642 (p0) cc_final: 0.8364 (p0) REVERT: S 5 MET cc_start: 0.7217 (mpp) cc_final: 0.6990 (mpp) REVERT: T 36 ASN cc_start: 0.7562 (m110) cc_final: 0.7037 (m-40) REVERT: U 25 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7964 (mtp85) REVERT: U 77 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8890 (mt-10) REVERT: V 16 MET cc_start: 0.7961 (mmm) cc_final: 0.7642 (mmm) REVERT: V 60 ILE cc_start: 0.8693 (mm) cc_final: 0.8469 (mm) REVERT: W 47 ARG cc_start: 0.7162 (mpt90) cc_final: 0.6910 (mmm-85) REVERT: W 54 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7815 (tp) REVERT: W 59 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7476 (tptp) REVERT: W 60 ARG cc_start: 0.7526 (ttm110) cc_final: 0.6776 (ptp-110) REVERT: X 31 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.7827 (tmm-80) REVERT: Z 36 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6319 (m-10) REVERT: Z 37 TYR cc_start: 0.7492 (t80) cc_final: 0.6999 (t80) REVERT: Z 38 GLU cc_start: 0.8142 (tp30) cc_final: 0.7787 (tp30) outliers start: 323 outliers final: 249 residues processed: 1428 average time/residue: 1.4132 time to fit residues: 3414.7253 Evaluate side-chains 1490 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1206 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 57 HIS Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 169 VAL Chi-restraints excluded: chain d residue 170 ARG Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 59 LYS Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 21 PHE Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 23 GLU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain u residue 86 PHE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 9.9990 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 50.0000 chunk 975 optimal weight: 10.0000 chunk 571 optimal weight: 0.0570 chunk 413 optimal weight: 9.9990 chunk 745 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 857 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 overall best weight: 6.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 ASN ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 163139 Z= 0.307 Angle : 0.785 12.801 244082 Z= 0.395 Chirality : 0.042 0.318 31220 Planarity : 0.006 0.069 13080 Dihedral : 24.423 179.061 81728 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 33.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.77 % Favored : 87.08 % Rotamer: Outliers : 6.44 % Allowed : 29.67 % Favored : 63.90 % 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: -3.13 (0.10), residues: 5919 helix: -1.15 (0.11), residues: 1819 sheet: -2.21 (0.16), residues: 899 loop : -2.65 (0.10), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 103 HIS 0.018 0.002 HIS Y 67 PHE 0.048 0.003 PHE l 50 TYR 0.024 0.002 TYR e 127 ARG 0.027 0.001 ARG b 237 *********************** 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 1546 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1230 time to evaluate : 5.814 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: 0.8370 (mtt180) cc_final: 0.8052 (mtt180) REVERT: b 57 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: b 163 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8597 (mm) REVERT: b 166 ARG cc_start: 0.8516 (ptp90) cc_final: 0.8175 (ptp90) REVERT: b 186 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: b 224 MET cc_start: 0.8775 (mmt) cc_final: 0.8458 (mmp) REVERT: c 1 MET cc_start: 0.6623 (ppp) cc_final: 0.6153 (ppp) REVERT: c 127 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: c 173 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: c 188 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8305 (mm) REVERT: d 29 HIS cc_start: 0.8200 (t-90) cc_final: 0.7430 (t-90) REVERT: d 61 ARG cc_start: 0.7932 (mpp-170) cc_final: 0.7429 (ptp90) REVERT: d 73 ILE cc_start: 0.8760 (tt) cc_final: 0.8155 (tt) REVERT: d 78 TRP cc_start: 0.8487 (m-10) cc_final: 0.8228 (m-10) REVERT: d 88 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7186 (mpt-90) REVERT: d 112 LEU cc_start: 0.9526 (mt) cc_final: 0.9141 (mt) REVERT: d 159 LEU cc_start: 0.7564 (mp) cc_final: 0.7195 (tp) REVERT: e 31 GLU cc_start: 0.8961 (tt0) cc_final: 0.8699 (tm-30) REVERT: e 129 MET cc_start: 0.7511 (ppp) cc_final: 0.7193 (ppp) REVERT: e 140 ILE cc_start: 0.6267 (mt) cc_final: 0.5917 (mp) REVERT: g 7 ASP cc_start: 0.8138 (m-30) cc_final: 0.7701 (m-30) REVERT: j 40 HIS cc_start: 0.8237 (p-80) cc_final: 0.7757 (p-80) REVERT: j 57 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6103 (pp) REVERT: j 69 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.7824 (tpp-160) REVERT: j 76 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8441 (p-80) REVERT: j 91 GLU cc_start: 0.8566 (tt0) cc_final: 0.8232 (tp30) REVERT: j 116 ARG cc_start: 0.7209 (ttt180) cc_final: 0.6806 (ttt180) REVERT: j 140 LEU cc_start: 0.7533 (tp) cc_final: 0.7240 (tt) REVERT: k 7 MET cc_start: 0.8227 (tpp) cc_final: 0.7877 (tpt) REVERT: k 12 ASP cc_start: 0.8546 (p0) cc_final: 0.8200 (p0) REVERT: k 40 LYS cc_start: 0.9338 (tppt) cc_final: 0.8956 (tptp) REVERT: k 58 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8805 (mm) REVERT: k 59 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8591 (mmtp) REVERT: k 64 ARG cc_start: 0.8715 (mtt90) cc_final: 0.8135 (mtt90) REVERT: l 3 LEU cc_start: 0.8162 (mp) cc_final: 0.7927 (mp) REVERT: l 10 GLU cc_start: 0.8793 (tp30) cc_final: 0.8262 (pt0) REVERT: l 41 ARG cc_start: 0.7065 (mmm-85) cc_final: 0.5919 (mmm-85) REVERT: l 55 MET cc_start: 0.8550 (mmt) cc_final: 0.8241 (tpp) REVERT: l 58 TYR cc_start: 0.8234 (p90) cc_final: 0.7810 (p90) REVERT: m 22 GLN cc_start: 0.1245 (OUTLIER) cc_final: -0.0085 (pt0) REVERT: m 68 PHE cc_start: 0.7715 (t80) cc_final: 0.7313 (t80) REVERT: m 117 PHE cc_start: 0.8891 (m-10) cc_final: 0.8478 (m-80) REVERT: n 13 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8296 (p0) REVERT: n 20 MET cc_start: 0.8236 (ppp) cc_final: 0.7200 (ppp) REVERT: n 24 MET cc_start: 0.8771 (ttp) cc_final: 0.8387 (ptm) REVERT: n 49 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8493 (mm-30) REVERT: n 112 TYR cc_start: 0.7521 (m-80) cc_final: 0.7155 (m-80) REVERT: o 18 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7983 (mm) REVERT: p 23 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7270 (t70) REVERT: p 43 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: p 61 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7692 (ttt90) REVERT: q 5 ARG cc_start: 0.7811 (ptt90) cc_final: 0.7182 (ptt-90) REVERT: q 13 HIS cc_start: 0.6885 (m170) cc_final: 0.6288 (m170) REVERT: q 23 TYR cc_start: 0.7730 (m-80) cc_final: 0.7496 (m-80) REVERT: q 56 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: r 13 ARG cc_start: 0.8033 (ptt90) cc_final: 0.7721 (tmm-80) REVERT: r 23 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: r 37 GLU cc_start: 0.5802 (pm20) cc_final: 0.5583 (pm20) REVERT: r 79 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8457 (ptt180) REVERT: r 86 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: s 48 LYS cc_start: 0.8965 (tttt) cc_final: 0.8515 (tttm) REVERT: s 69 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7544 (mt) REVERT: u 97 SER cc_start: 0.8526 (t) cc_final: 0.8068 (p) REVERT: v 2 PHE cc_start: 0.5703 (m-10) cc_final: 0.5374 (m-10) REVERT: v 26 PHE cc_start: 0.7539 (p90) cc_final: 0.7131 (p90) REVERT: v 56 PHE cc_start: 0.7713 (t80) cc_final: 0.6776 (t80) REVERT: x 33 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.6547 (m-70) REVERT: x 36 ARG cc_start: 0.5947 (ptm-80) cc_final: 0.5473 (ptm-80) REVERT: y 1 MET cc_start: 0.8570 (mtm) cc_final: 0.8334 (mtm) REVERT: y 17 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6156 (tt0) REVERT: y 24 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: y 25 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8484 (tm-30) REVERT: y 30 MET cc_start: 0.7812 (mmp) cc_final: 0.7399 (mmp) REVERT: z 44 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8265 (mmm160) REVERT: B 16 ARG cc_start: 0.9280 (mtt180) cc_final: 0.8310 (mtt90) REVERT: D 13 ASN cc_start: 0.8864 (m110) cc_final: 0.8571 (m110) REVERT: D 19 ARG cc_start: 0.8980 (mtp180) cc_final: 0.8583 (ttp-170) REVERT: E 2 LYS cc_start: 0.8340 (mttt) cc_final: 0.7968 (mtpt) REVERT: E 15 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7267 (ttpt) REVERT: E 43 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8425 (mm) REVERT: G 15 PHE cc_start: 0.9122 (m-80) cc_final: 0.8753 (m-80) REVERT: G 19 THR cc_start: 0.2796 (OUTLIER) cc_final: 0.2487 (p) REVERT: G 21 TYR cc_start: 0.8330 (m-80) cc_final: 0.7858 (m-80) REVERT: G 77 GLU cc_start: 0.8447 (pp20) cc_final: 0.8046 (pp20) REVERT: G 80 LYS cc_start: 0.8511 (tmmt) cc_final: 0.8224 (tmmt) REVERT: G 164 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.6101 (m-30) REVERT: G 173 LYS cc_start: 0.9132 (tttt) cc_final: 0.8772 (pttp) REVERT: G 207 ARG cc_start: 0.9040 (ptt-90) cc_final: 0.8395 (ptp90) REVERT: G 211 LEU cc_start: 0.9444 (tt) cc_final: 0.9204 (mt) REVERT: G 212 TYR cc_start: 0.8093 (m-10) cc_final: 0.7793 (m-10) REVERT: H 39 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7703 (mmm160) REVERT: H 55 VAL cc_start: 0.8546 (t) cc_final: 0.8191 (m) REVERT: H 184 ASN cc_start: 0.7148 (t0) cc_final: 0.6471 (t0) REVERT: I 61 ARG cc_start: 0.7896 (mtp85) cc_final: 0.5640 (mtp85) REVERT: I 74 TYR cc_start: 0.7854 (m-80) cc_final: 0.6976 (m-80) REVERT: I 87 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6868 (pp20) REVERT: I 162 GLU cc_start: 0.8834 (tp30) cc_final: 0.8592 (mp0) REVERT: I 195 ASN cc_start: 0.7557 (t0) cc_final: 0.7283 (t0) REVERT: J 25 LYS cc_start: 0.8081 (tptt) cc_final: 0.7777 (tptp) REVERT: J 49 TYR cc_start: 0.7937 (t80) cc_final: 0.7710 (t80) REVERT: J 92 ARG cc_start: 0.7473 (mtm180) cc_final: 0.7106 (mtm180) REVERT: J 110 MET cc_start: 0.8068 (mpp) cc_final: 0.7422 (mpp) REVERT: J 133 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5535 (tp) REVERT: K 1 MET cc_start: 0.6860 (tmm) cc_final: 0.5223 (tpp) REVERT: L 73 GLU cc_start: 0.9236 (pt0) cc_final: 0.8574 (pp20) REVERT: L 89 GLU cc_start: 0.8247 (tp30) cc_final: 0.7954 (tp30) REVERT: M 14 ARG cc_start: 0.7484 (ttm110) cc_final: 0.6473 (mtp180) REVERT: M 53 ASP cc_start: 0.8540 (p0) cc_final: 0.8266 (p0) REVERT: M 61 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7605 (p) REVERT: M 86 LYS cc_start: 0.8508 (mmtt) cc_final: 0.6891 (mmmt) REVERT: M 90 GLU cc_start: 0.8440 (tt0) cc_final: 0.7836 (tm-30) REVERT: N 48 ARG cc_start: 0.6685 (ptt-90) cc_final: 0.6078 (ttm-80) REVERT: N 89 TYR cc_start: 0.5431 (m-80) cc_final: 0.4983 (m-80) REVERT: O 5 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7654 (ttm110) REVERT: O 63 ASP cc_start: 0.8807 (m-30) cc_final: 0.8576 (m-30) REVERT: O 88 MET cc_start: 0.8921 (pmm) cc_final: 0.8647 (pmm) REVERT: P 37 GLN cc_start: 0.8464 (tp40) cc_final: 0.7968 (tm-30) REVERT: P 39 ASN cc_start: 0.8306 (m110) cc_final: 0.7260 (m-40) REVERT: Q 4 ASN cc_start: 0.7848 (t0) cc_final: 0.7499 (t0) REVERT: Q 45 ASN cc_start: 0.6642 (m-40) cc_final: 0.6317 (m-40) REVERT: R 49 GLU cc_start: 0.7828 (tp30) cc_final: 0.7384 (tp30) REVERT: R 53 ASP cc_start: 0.8648 (p0) cc_final: 0.8367 (p0) REVERT: S 5 MET cc_start: 0.7294 (mpp) cc_final: 0.7021 (mpp) REVERT: T 16 ARG cc_start: 0.7841 (mmp80) cc_final: 0.7613 (mmp80) REVERT: T 36 ASN cc_start: 0.7542 (m110) cc_final: 0.6999 (m-40) REVERT: U 25 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7925 (mtp85) REVERT: U 77 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8888 (mt-10) REVERT: V 16 MET cc_start: 0.7904 (mmm) cc_final: 0.7613 (mmm) REVERT: W 47 ARG cc_start: 0.7077 (mpt90) cc_final: 0.6738 (mmm-85) REVERT: W 54 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7835 (tp) REVERT: W 59 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7487 (tptp) REVERT: W 60 ARG cc_start: 0.7617 (ttm110) cc_final: 0.6893 (ptp-110) REVERT: X 31 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.7954 (tmm-80) REVERT: Z 15 LEU cc_start: 0.9420 (tt) cc_final: 0.9013 (mp) REVERT: Z 36 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: Z 37 TYR cc_start: 0.7523 (t80) cc_final: 0.7032 (t80) REVERT: Z 38 GLU cc_start: 0.8179 (tp30) cc_final: 0.7807 (tp30) outliers start: 316 outliers final: 248 residues processed: 1418 average time/residue: 1.3490 time to fit residues: 3229.6754 Evaluate side-chains 1478 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1197 time to evaluate : 8.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 57 HIS Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 112 LYS Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 116 MET Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 59 LYS Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 23 GLU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 94 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 61 GLU Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE 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: 20.0000 chunk 476 optimal weight: 8.9990 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 838 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 647 optimal weight: 20.0000 overall best weight: 11.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 55 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 163139 Z= 0.492 Angle : 1.036 14.230 244082 Z= 0.514 Chirality : 0.052 0.314 31220 Planarity : 0.008 0.142 13080 Dihedral : 25.078 178.873 81728 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 49.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.80 % Favored : 84.96 % Rotamer: Outliers : 6.64 % Allowed : 29.28 % Favored : 64.08 % 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: -3.58 (0.10), residues: 5919 helix: -1.60 (0.11), residues: 1801 sheet: -2.42 (0.16), residues: 858 loop : -2.90 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 103 HIS 0.019 0.003 HIS B 18 PHE 0.052 0.004 PHE l 50 TYR 0.028 0.003 TYR K 25 ARG 0.032 0.001 ARG J 68 ********************** 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 1522 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1196 time to evaluate : 6.336 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: b 57 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.6990 (t-90) REVERT: b 166 ARG cc_start: 0.8720 (ptp90) cc_final: 0.8429 (ptp90) REVERT: b 186 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: b 237 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7344 (mtt180) REVERT: b 263 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: c 40 LEU cc_start: 0.7912 (mp) cc_final: 0.7344 (mt) REVERT: c 127 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: c 173 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: c 188 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (mm) REVERT: d 21 ARG cc_start: 0.8705 (ttm170) cc_final: 0.7855 (ttt180) REVERT: d 29 HIS cc_start: 0.8249 (t-90) cc_final: 0.7427 (t70) REVERT: d 61 ARG cc_start: 0.7917 (mpp-170) cc_final: 0.7681 (mtm-85) REVERT: d 73 ILE cc_start: 0.8912 (tt) cc_final: 0.8289 (tt) REVERT: d 78 TRP cc_start: 0.8612 (m-10) cc_final: 0.8105 (m-10) REVERT: d 88 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7341 (mpt-90) REVERT: d 112 LEU cc_start: 0.9499 (mt) cc_final: 0.9098 (mt) REVERT: e 31 GLU cc_start: 0.8955 (tt0) cc_final: 0.8716 (tm-30) REVERT: e 140 ILE cc_start: 0.6158 (mt) cc_final: 0.5821 (mp) REVERT: g 7 ASP cc_start: 0.8032 (m-30) cc_final: 0.7695 (m-30) REVERT: h 52 MET cc_start: -0.0599 (ttm) cc_final: -0.0822 (mtt) REVERT: j 2 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8696 (mtmt) REVERT: j 40 HIS cc_start: 0.8351 (p-80) cc_final: 0.8116 (p-80) REVERT: j 57 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6174 (pp) REVERT: j 69 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.7970 (tpp-160) REVERT: j 76 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8487 (p-80) REVERT: j 91 GLU cc_start: 0.8865 (tt0) cc_final: 0.8600 (mm-30) REVERT: j 116 ARG cc_start: 0.7097 (ttt180) cc_final: 0.6794 (ttt180) REVERT: k 12 ASP cc_start: 0.8480 (p0) cc_final: 0.8096 (p0) REVERT: l 10 GLU cc_start: 0.8813 (tp30) cc_final: 0.8324 (pt0) REVERT: l 41 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6437 (mmm-85) REVERT: l 55 MET cc_start: 0.8573 (mmt) cc_final: 0.8272 (tpp) REVERT: l 58 TYR cc_start: 0.8143 (p90) cc_final: 0.7693 (p90) REVERT: m 22 GLN cc_start: 0.1438 (OUTLIER) cc_final: 0.0560 (pt0) REVERT: m 68 PHE cc_start: 0.8037 (t80) cc_final: 0.7821 (t80) REVERT: m 117 PHE cc_start: 0.8898 (m-10) cc_final: 0.8595 (m-80) REVERT: n 13 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8335 (p0) REVERT: n 20 MET cc_start: 0.8236 (ppp) cc_final: 0.7013 (ppp) REVERT: n 24 MET cc_start: 0.8796 (ttp) cc_final: 0.8456 (ptm) REVERT: n 32 GLU cc_start: 0.7088 (tt0) cc_final: 0.6794 (tm-30) REVERT: n 43 GLU cc_start: 0.8787 (tp30) cc_final: 0.8108 (tp30) REVERT: n 49 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8646 (mm-30) REVERT: n 112 TYR cc_start: 0.7644 (m-80) cc_final: 0.7218 (m-80) REVERT: o 18 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7777 (mm) REVERT: p 23 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7466 (t0) REVERT: p 43 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: p 61 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7731 (ttt90) REVERT: q 5 ARG cc_start: 0.7820 (ptt90) cc_final: 0.7443 (ptt-90) REVERT: q 35 PHE cc_start: 0.8677 (t80) cc_final: 0.7656 (t80) REVERT: q 51 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8467 (tp40) REVERT: q 56 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.5894 (m-10) REVERT: r 23 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: r 79 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8566 (ptt180) REVERT: r 86 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: s 8 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7498 (mtm110) REVERT: s 48 LYS cc_start: 0.9008 (tttt) cc_final: 0.8579 (ttmt) REVERT: u 97 SER cc_start: 0.8517 (t) cc_final: 0.8092 (p) REVERT: v 26 PHE cc_start: 0.7840 (p90) cc_final: 0.7408 (p90) REVERT: x 33 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6507 (m-70) REVERT: y 1 MET cc_start: 0.8620 (mtm) cc_final: 0.8116 (mtm) REVERT: y 18 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (mt) REVERT: y 24 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: y 30 MET cc_start: 0.8025 (mmp) cc_final: 0.7820 (mmp) REVERT: B 16 ARG cc_start: 0.9257 (mtt180) cc_final: 0.8379 (mtt90) REVERT: E 2 LYS cc_start: 0.8399 (mttt) cc_final: 0.8069 (mtpt) REVERT: E 43 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8491 (mm) REVERT: E 46 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: F 15 LYS cc_start: 0.6168 (mmtt) cc_final: 0.5149 (mmtt) REVERT: G 15 PHE cc_start: 0.9071 (m-80) cc_final: 0.8784 (m-80) REVERT: G 19 THR cc_start: 0.2932 (OUTLIER) cc_final: 0.2631 (p) REVERT: G 21 TYR cc_start: 0.8399 (m-80) cc_final: 0.7921 (m-80) REVERT: G 44 LYS cc_start: 0.5167 (OUTLIER) cc_final: 0.4898 (mttt) REVERT: G 77 GLU cc_start: 0.8502 (pp20) cc_final: 0.8144 (pp20) REVERT: G 80 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8490 (tmmt) REVERT: G 173 LYS cc_start: 0.9208 (tttt) cc_final: 0.8847 (pttp) REVERT: G 207 ARG cc_start: 0.9125 (ptt-90) cc_final: 0.8805 (mpp-170) REVERT: G 211 LEU cc_start: 0.9450 (tt) cc_final: 0.9230 (mt) REVERT: G 212 TYR cc_start: 0.8260 (m-10) cc_final: 0.7942 (m-10) REVERT: H 39 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.6868 (mtp-110) REVERT: H 184 ASN cc_start: 0.7184 (t0) cc_final: 0.6451 (t0) REVERT: I 74 TYR cc_start: 0.8060 (m-80) cc_final: 0.7173 (m-80) REVERT: I 87 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: I 131 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5754 (tp) REVERT: J 25 LYS cc_start: 0.8208 (tptt) cc_final: 0.7616 (tptp) REVERT: J 49 TYR cc_start: 0.8092 (t80) cc_final: 0.7807 (t80) REVERT: J 70 MET cc_start: 0.8478 (mtt) cc_final: 0.8146 (mtp) REVERT: J 92 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7258 (mtm180) REVERT: J 110 MET cc_start: 0.8160 (mpp) cc_final: 0.7498 (mpp) REVERT: K 1 MET cc_start: 0.7483 (tmm) cc_final: 0.7123 (tmm) REVERT: L 25 PHE cc_start: 0.8902 (m-80) cc_final: 0.8373 (m-80) REVERT: L 73 GLU cc_start: 0.9342 (pt0) cc_final: 0.8660 (pp20) REVERT: L 89 GLU cc_start: 0.8110 (tp30) cc_final: 0.7820 (tp30) REVERT: L 100 MET cc_start: 0.9016 (mmt) cc_final: 0.8505 (mpp) REVERT: M 14 ARG cc_start: 0.7499 (ttm110) cc_final: 0.6608 (mtp180) REVERT: M 47 ASP cc_start: 0.8664 (t0) cc_final: 0.8382 (t0) REVERT: M 49 LYS cc_start: 0.8970 (tttt) cc_final: 0.8616 (tttp) REVERT: M 53 ASP cc_start: 0.8576 (p0) cc_final: 0.8282 (p0) REVERT: M 61 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7879 (p) REVERT: M 63 LYS cc_start: 0.7982 (mttp) cc_final: 0.7316 (mttm) REVERT: N 48 ARG cc_start: 0.6724 (ptt-90) cc_final: 0.5971 (ttm-80) REVERT: N 59 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8557 (mmmt) REVERT: N 89 TYR cc_start: 0.5663 (m-80) cc_final: 0.5295 (m-80) REVERT: O 63 ASP cc_start: 0.8667 (m-30) cc_final: 0.8289 (m-30) REVERT: P 37 GLN cc_start: 0.8452 (tp40) cc_final: 0.7855 (tm-30) REVERT: P 39 ASN cc_start: 0.8283 (m110) cc_final: 0.7110 (m-40) REVERT: Q 4 ASN cc_start: 0.7956 (t0) cc_final: 0.7583 (t0) REVERT: Q 45 ASN cc_start: 0.7228 (m-40) cc_final: 0.6918 (m-40) REVERT: R 49 GLU cc_start: 0.7771 (tp30) cc_final: 0.7318 (tp30) REVERT: R 53 ASP cc_start: 0.8739 (p0) cc_final: 0.8463 (p0) REVERT: R 71 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8882 (pt0) REVERT: R 102 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8621 (ttpp) REVERT: T 36 ASN cc_start: 0.7701 (m110) cc_final: 0.7193 (m-40) REVERT: T 57 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7294 (ppt170) REVERT: U 25 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8060 (mtp85) REVERT: U 77 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8806 (mt-10) REVERT: V 10 ARG cc_start: 0.9089 (tpt-90) cc_final: 0.8621 (tpp80) REVERT: V 16 MET cc_start: 0.7824 (mmm) cc_final: 0.7447 (mmm) REVERT: W 54 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (tp) REVERT: W 59 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7385 (tptp) REVERT: W 60 ARG cc_start: 0.7662 (ttm110) cc_final: 0.6945 (ptp-110) REVERT: X 31 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8057 (tmm-80) REVERT: X 77 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6160 (mtt90) REVERT: Y 17 ARG cc_start: 0.9238 (ptm-80) cc_final: 0.8738 (ptm-80) REVERT: Z 37 TYR cc_start: 0.7337 (t80) cc_final: 0.7057 (t80) REVERT: Z 38 GLU cc_start: 0.8305 (tp30) cc_final: 0.7887 (tp30) outliers start: 326 outliers final: 264 residues processed: 1393 average time/residue: 1.3773 time to fit residues: 3253.8572 Evaluate side-chains 1453 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1155 time to evaluate : 6.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 57 HIS Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 175 LEU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 228 ASP Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain b residue 242 HIS Chi-restraints excluded: chain b residue 244 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 127 PHE Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain c residue 148 GLN Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 72 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 105 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 158 PHE Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain e residue 173 ASP Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 172 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 112 LYS Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 118 ILE Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 16 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 67 ASN Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 77 HIS Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 84 CYS Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 35 HIS Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 96 LYS Chi-restraints excluded: chain l residue 107 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 31 PHE Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 13 ASN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 17 ARG Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 2 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 97 PHE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 43 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 36 GLN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 56 PHE Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 23 GLU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain r residue 102 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 82 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 33 HIS Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 13 GLU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain y residue 24 GLU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 43 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 33 HIS Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 55 ARG Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 120 CYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 70 HIS Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 49 LYS Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 TYR Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 18 PHE Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 0.8980 chunk 666 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 839 optimal weight: 40.0000 chunk 351 optimal weight: 5.9990 chunk 862 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 149 ASN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 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** I 70 GLN J 60 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.109272 restraints weight = 527264.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.112224 restraints weight = 200199.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.113051 restraints weight = 102415.497| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 163139 Z= 0.266 Angle : 0.786 14.370 244082 Z= 0.397 Chirality : 0.042 0.379 31220 Planarity : 0.006 0.098 13080 Dihedral : 24.729 178.543 81728 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 33.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.21 % Favored : 87.63 % Rotamer: Outliers : 5.83 % Allowed : 30.81 % Favored : 63.37 % 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: -3.28 (0.10), residues: 5919 helix: -1.35 (0.11), residues: 1816 sheet: -2.23 (0.16), residues: 877 loop : -2.73 (0.10), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 103 HIS 0.019 0.002 HIS j 47 PHE 0.049 0.003 PHE V 27 TYR 0.026 0.002 TYR e 127 ARG 0.027 0.001 ARG q 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45589.92 seconds wall clock time: 796 minutes 29.75 seconds (47789.75 seconds total)